Source code for tests.test_formats_dicom_template

import unittest
import os.path
from datetime import datetime, timezone
import numpy as np
import tempfile
import argparse

import imagedata.cmdline as cmdline
import imagedata.formats as formats
from imagedata.series import Series
from tests.compare_headers import compare_headers, compare_template_headers, compare_geometry_headers




class ShouldHaveFailed(Exception):
    pass





class TestDicomTemplate(unittest.TestCase):


    def setUp(self):
        parser = argparse.ArgumentParser()
        cmdline.add_argparse_options(parser)

        self.opts = parser.parse_args(['--of', 'dicom'])
        self.opts_template = parser.parse_args(['--of', 'dicom',
                                                '--input_options', 'AcceptDuplicateTag=True',
                                                '--template', 'data/dicom/time/time00/'])
        self.opts_geometry = parser.parse_args(['--of', 'dicom',
                                                '--input_options', 'AcceptDuplicateTag=True',
                                                '--geometry', 'data/dicom/time/time00/'])
        self.opts_tempgeom = parser.parse_args(['--of', 'dicom',
                                                '--input_options', 'AcceptDuplicateTag=True',
                                                '--template', 'data/dicom/time/time00/',
                                                '--geometry', 'data/dicom/time/time00/'])

        plugins = formats.get_plugins_list()
        self.dicom_plugin = None
        for pname, ptype, pclass in plugins:
            if ptype == 'dicom':
                self.dicom_plugin = pclass
        self.assertIsNotNone(self.dicom_plugin)




    def getEmpty(self, dir):
        # Create a DICOM series with empty header
        si0 = Series(os.path.join('data', 'mat', 'time', 'Image_00000.mat'),
                     input_order='time', input_format='mat')
        si00 = Series(si0[0], input_order='none')
        si00.write(dir, formats=['dicom'])




    def getEmptyTime(self, dir):
        # Provide sensible time tags
        si0 = Series(os.path.join('data', 'mat', 'time', 'Image_00000.mat'),
                     input_order='time', input_format='mat')
        si01 = Series(si0[:2], input_order='time')
        for s in range(3):
            for t in range(2):
                time_str = datetime.fromtimestamp(float(t), timezone.utc).strftime("%H%M%S.%f")
                si01.setDicomAttribute('AcquisitionTime', time_str, slice=s, tag=t)
        si01.write(dir, formats=['dicom'])




    def test_dicom_template_cmdline(self):
        # Read the DICOM empty header series,
        # adding DICOM template
        with tempfile.TemporaryDirectory() as emptydir:
            self.getEmpty(emptydir)
            si1 = Series(emptydir, 'none', self.opts_template, input_format='dicom')
        # Read the original DICOM series
        si2 = Series(os.path.join('data', 'dicom', 'time', 'time00'), input_format='dicom')
        # Compare constructed series si1 to original series si2
        self.assertEqual(si1.dtype, si2.dtype)
        np.testing.assert_array_equal(si1, si2)
        compare_template_headers(self, si1, si2)
        try:
            compare_geometry_headers(self, si1, si2)
        except AssertionError:
            # Expected to fail
            pass
        else:
            raise ShouldHaveFailed('Template header should differ when joining geometry')
        # Write constructed series si1 to disk,
        # then re-read and compare to original si2
        with tempfile.TemporaryDirectory() as d:
            si1.write(d, formats=['dicom'])
            si3 = Series(d, 'none', self.opts, input_format='dicom')
        np.testing.assert_array_equal(si2, si3)
        compare_template_headers(self, si2, si3)




    def test_dicom_template_prog(self):
        # Read the DICOM empty header series,
        # adding DICOM template in Series constructor
        template = Series(os.path.join('data', 'dicom', 'time', 'time00'), input_format='dicom')
        with tempfile.TemporaryDirectory() as emptydir:
            self.getEmpty(emptydir)
            si1 = Series(
                emptydir,
                template=template,
                input_format='dicom')
        si2 = Series(os.path.join('data', 'dicom', 'time', 'time00'), input_format='dicom')
        # Compare constructed series si1 to original series si2
        self.assertEqual(si1.dtype, si2.dtype)
        np.testing.assert_array_equal(si1, si2)
        compare_template_headers(self, si1, si2)




    def test_dicom_geometry_cmdline(self):
        # Read the DICOM empty header series,
        # adding DICOM geometry
        with tempfile.TemporaryDirectory() as emptydir:
            self.getEmpty(emptydir)
            si1 = Series(emptydir, 'none', self.opts_geometry, input_format='dicom')
        # Read the original DICOM series
        si2 = Series(os.path.join('data', 'dicom', 'time', 'time00'), input_format='dicom')
        # Compare constructed series si1 to original series si2
        self.assertEqual(si1.dtype, si2.dtype)
        np.testing.assert_array_equal(si1, si2)
        compare_geometry_headers(self, si1, si2)
        try:
            compare_template_headers(self, si1, si2)
        except AssertionError:
            # Expected to fail
            pass
        else:
            raise ShouldHaveFailed('Template header should differ when joining geometry')
        # Write constructed series si1 to disk,
        # then re-read and compare to original si2
        with tempfile.TemporaryDirectory() as d:
            si1.write(d, formats=['dicom'])
            si3 = Series(d, 'none', self.opts, input_format='dicom')
        np.testing.assert_array_equal(si2, si3)
        compare_geometry_headers(self, si2, si2)




    def test_dicom_geometry_prog(self):
        # Read the DICOM empty header series,
        # adding DICOM geometry in Series constructor
        geometry = Series(os.path.join('data', 'dicom', 'time', 'time00'), input_format='dicom')
        with tempfile.TemporaryDirectory() as emptydir:
            self.getEmpty(emptydir)
            si1 = Series(emptydir, geometry=geometry, input_format='dicom')
        si2 = Series(os.path.join('data', 'dicom', 'time', 'time00'), input_format='dicom')
        # Compare constructed series si1 to original series si2
        self.assertEqual(si1.dtype, si2.dtype)
        np.testing.assert_array_equal(si1, si2)
        compare_geometry_headers(self, si1, si2)
        try:
            compare_template_headers(self, si1, si2)
        except AssertionError:
            # Expected to fail
            pass
        else:
            raise ShouldHaveFailed('Template header should differ when joining geometry')




    def test_dicom_tempgeom_cmdline(self):
        # Read the DICOM empty header series,
        # adding DICOM template
        with tempfile.TemporaryDirectory() as emptydir:
            self.getEmpty(emptydir)
            si1 = Series(emptydir, 'none', self.opts_tempgeom, input_format='dicom')
        # Read the original DICOM series
        si2 = Series(os.path.join('data', 'dicom', 'time', 'time00'), input_format='dicom')
        # Compare constructed series si1 to original series si2
        self.assertEqual(si1.dtype, si2.dtype)
        np.testing.assert_array_equal(si1, si2)
        compare_headers(self, si1, si2)
        # Write constructed series si1 to disk,
        # then re-read and compare to original si2
        with tempfile.TemporaryDirectory() as d:
            si1.write(d, formats=['dicom'])
            si3 = Series(d, 'none', self.opts, input_format='dicom')
        np.testing.assert_array_equal(si2, si3)
        compare_headers(self, si2, si3)




    def test_dicom_tempgeom_prog(self):
        # Read the DICOM empty header series,
        # adding DICOM template in Series constructor
        template = Series(os.path.join('data', 'dicom', 'time', 'time00'), input_format='dicom')
        geometry = Series(os.path.join('data', 'dicom', 'time', 'time00'), input_format='dicom')
        with tempfile.TemporaryDirectory() as emptydir:
            self.getEmpty(emptydir)
            si1 = Series(emptydir, template=template, geometry=geometry, input_format='dicom')
        si2 = Series(os.path.join('data', 'dicom', 'time', 'time00'), input_format='dicom')
        # Compare constructed series si1 to original series si2
        self.assertEqual(si1.dtype, si2.dtype)
        np.testing.assert_array_equal(si1, si2)
        compare_headers(self, si1, si2)




    def test_dicom_temp_slice(self):
        # Read the DICOM empty header series,
        # adding DICOM template in Series constructor
        # Then slice the si1 Series
        template = Series(os.path.join('data', 'dicom', 'time'), input_order='time', input_format='dicom')
        geometry = Series(os.path.join('data', 'dicom', 'time'), input_order='time', input_format='dicom')
        with tempfile.TemporaryDirectory() as emptydir:
            self.getEmptyTime(emptydir)
            si1 = Series(emptydir, input_order='time', template=template, geometry=geometry, input_format='dicom')
        si1_0 = si1[0]
        si2 = Series(os.path.join('data', 'dicom', 'time', 'time00'), input_format='dicom')
        # Compare constructed series si1_0 to original series si2
        self.assertEqual(si1_0.dtype, si2.dtype)
        np.testing.assert_array_equal(si1_0, si2)
        # Tags do not match, so copy them to enable header comparison.
        si1_0.tags = si2.tags
        compare_headers(self, si1_0, si2)






class TestDicomGeometryTemplate(unittest.TestCase):


    def setUp(self):
        parser = argparse.ArgumentParser()
        cmdline.add_argparse_options(parser)

        self.opts = parser.parse_args(['--of', 'dicom'])
        self.opts_template = parser.parse_args(['--of', 'dicom',
                                                '--input_options', 'AcceptDuplicateTag=True',
                                                '--template', 'data/dicom/time/time00/'])
        self.opts_geometry = parser.parse_args(['--of', 'dicom',
                                                '--input_options', 'AcceptDuplicateTag=True',
                                                '--geometry', 'data/dicom/time/time00/'])
        self.opts_tempgeom = parser.parse_args(['--of', 'dicom',
                                                '--input_options', 'AcceptDuplicateTag=True',
                                                '--template', 'data/dicom/time/time00/',
                                                '--geometry', 'data/dicom/time/time00/'])

        plugins = formats.get_plugins_list()
        self.dicom_plugin = None
        for pname, ptype, pclass in plugins:
            if ptype == 'dicom':
                self.dicom_plugin = pclass
        self.assertIsNotNone(self.dicom_plugin)




    def test_dicom_too_many_template_slices(self):
        # Construct simple series,
        # add DICOM template in Series constructor
        template = Series(os.path.join('data', 'dicom', 'time', 'time00'), input_format='dicom')
        si1 = Series(
            np.zeros((2, 192, 152)),
            geometry=template)
        # Compare constructed series si1 to original series template
        np.testing.assert_array_equal(template.sliceLocations[:2], si1.sliceLocations)




    def test_dicom_too_few_template_slices(self):
        # Construct simple series,
        # add DICOM template in Series constructor
        template = Series(os.path.join('data', 'dicom', 'time', 'time00'), input_format='dicom')
        # Add an extra slice
        shape = (template.shape[0]+1, template.shape[1], template.shape[2])
        si1 = Series(np.zeros(shape), geometry=template, input_format='dicom')
        # Compare constructed series si1 to original series template
        # Append one slice location to template
        ds = template.sliceLocations[1] - template.sliceLocations[0]
        ns = template.sliceLocations[-1] + ds
        template_list = template.sliceLocations.tolist()
        template_list.append(ns)
        template_locations = np.array(template_list)
        np.testing.assert_array_equal(template_locations, si1.sliceLocations)




    def test_dicom_too_many_template_tags(self):
        # Construct simple series,
        # add DICOM template in Series constructor
        template = Series(os.path.join('data', 'dicom', 'time'), 'time', input_format='dicom')
        si1 = Series(
            np.zeros((2, 3, 192, 152)),
            template=template, geometry=template)
        # Compare constructed series si1 to original series template
        for _slice in range(3):
            np.testing.assert_array_equal(template.tags[_slice][:2], si1.tags[_slice])




    def test_dicom_too_few_template_tags(self):
        # Construct simple series,
        # add DICOM template in Series constructor
        template = Series(os.path.join('data', 'dicom', 'time'), 'time', input_format='dicom')
        si1 = Series(
            np.zeros((template.shape[0]+1, template.shape[1],
                      template.shape[2], template.shape[3])),
            'time',
            template=template, geometry=template)
        # Compare constructed series si1 to original series template
        for _slice in range(si1.slices):
            # Append one time point to template
            ds = template.tags[_slice][1][0] - template.tags[_slice][0][0]
            ns = template.tags[_slice][-1][0] + ds
            si1_tags_arr = np.empty(si1.shape[0], dtype=float)
            for _ in range(si1.shape[0]):
                si1_tags_arr[_] = si1.tags[_slice][_][0]
            template_arr = np.empty(template.shape[0]+1, dtype=float)
            for _ in range(template.shape[0]):
                template_arr[_] = template.tags[_slice][_][0]
            template_arr[-1] = ns
            np.testing.assert_array_almost_equal(si1_tags_arr, template_arr, decimal=4)
            np.testing.assert_array_almost_equal(si1.axes[0].values, template_arr, decimal=4)




if __name__ == '__main__':
    unittest.main()