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Build # 799

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travis-ci

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bastula

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<a href="https://github.com/dicompyler/dicompyler-core/commit/<a class=hub.com/dicompyler/dicompyler-core/commit/9db5f239952b6a303635ac54be836238af5e0b7a">9db5f2399<a href="https://github.com/dicompyler/dicompyler-core/commit/9db5f239952b6a303635ac54be836238af5e0b7a">&quot;&gt;Merge commit &amp;#39;&lt;/a&gt;&lt;a class=&quot;double-link&quot; href=&quot;https://github.com/dicompyler/dicompyler-core/commit/&lt;a class=&quot;double-link&quot; href=&quot;https://git">&lt;a class=</a>hub.com/dicompyler/dicompyler-core/commit/<a class=hub.com/dicompyler/dicompyler-core/commit/4855d79b7729e6277e09a8a1a09399c30142a8ad">4855d79b7">4855d79b7</a><a href="https://github.com/dicompyler/dicompyler-core/commit/9db5f239952b6a303635ac54be836238af5e0b7a">&#39; into dose

* commit &#39;4855d79b7729e6277e09a8a1a09399c30142a8ad&#39;:
  rename summation_post_processing to dose_grid_post_processing, minor reorganization
  remove points property, raise error on negative doses
  DoseGrid examples
  test modality check, save_dcm. minor edits.</a>

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89.57

/dicompylercore/dose.py

#!/usr/bin/env python
# -*- coding: utf-8 -*-
# dose.py
"""Routines to access and modify DICOM RT Dose."""
# Copyright (c) 2009-2016 Aditya Panchal
# Copyright (c) 2019-2020 Dan Cutright
# This file is part of dicompyler-core, released under a BSD license.
#    See the file license.txt included with this distribution, also
#    available at https://github.com/dicompyler/dicompyler-core/
#
# This code was adapted from dicom_dose_sum.py from DVH Analytics:
#    https://github.com/cutright/DVH-Analytics/

from copy import deepcopy
import numpy as np
from dicompylercore import dicomparser
from pydicom.uid import generate_uid
from pydicom.datadict import dictionary_VR, keyword_dict
from dicompylercore.config import dicompyler_uid_prefix_rtdose, scipy_available
from datetime import datetime
from pydicom.sequence import Sequence
from pydicom.dataset import Dataset
from warnings import warn

if scipy_available:
    from scipy.ndimage import map_coordinates


class DoseGrid:
    """
    Class to easily access commonly used attributes of a DICOM dose grid and
    make modifications

    Example: Add two dose grids
        grid_1 = DoseGrid(dose_file_1)
        grid_2 = DoseGrid(dose_file_2)
        grid_sum = grid_1 + grid_2
        grid_sum.save_dcm(some_file_path)

    """

    def __init__(self, rt_dose, order=1):
        """ Initialization of a DoseGrid from a DICOM-RT Dose file or dataset.

        Parameters
        ----------
        rt_dose : pydicom Dataset or filename
            DICOM RT Dose used to determine the structure dose grid data.
        order : int, optional
            The order of the spline interpolation.
            0: the nearest grid point, 1: trilinear, 2 to 5: spline
        """

        self.ds = dicomparser.DicomParser(rt_dose).ds
        self.order = order

        self.summation_type = None
        self.sop_class_uid = self.ds.SOPClassUID
        self.sop_instance_uid = self.ds.SOPInstanceUID
        self.other_sop_class_uid = None
        self.other_sop_instance_uid = None

        if self.ds.Modality == "RTDOSE":
            self.x_axis = (
                np.arange(self.ds.Columns) * self.ds.PixelSpacing[0]
                + self.ds.ImagePositionPatient[0]
            )
            self.y_axis = (
                np.arange(self.ds.Rows) * self.ds.PixelSpacing[1]
                + self.ds.ImagePositionPatient[1]
            )
            self.z_axis = (
                np.array(self.ds.GridFrameOffsetVector)
                + self.ds.ImagePositionPatient[2]
            )

            # x and z are swapped in the pixel_array
            pixel_array = self.ds.pixel_array * self.ds.DoseGridScaling
            self.dose_grid = np.swapaxes(pixel_array, 0, 2)
        else:
            raise AttributeError(
                "The DoseGrid class requires an RTDOSE file or dataset. "
                "%s was detected" % self.ds.Modality
            )

    ####################################################
    # Basic properties
    ####################################################
    @property
    def shape(self):
        """Get the x, y, z dimensions of the dose grid"""
        return (
            self.ds.Columns,
            self.ds.Rows,
            len(self.ds.GridFrameOffsetVector),
        )

    @property
    def axes(self):
        """Get the x, y, z axes of the dose grid (in mm)"""
        return [self.x_axis, self.y_axis, self.z_axis]

    @property
    def scale(self):
        """Get the dose grid resolution (xyz)"""
        if np.any(np.diff(np.diff(self.ds.GridFrameOffsetVector))):
            raise NotImplementedError(
                "Non-uniform GridFrameOffsetVector detected. Interpolated "
                "summation of non-uniform dose-grid scales is not supported."
            )
        return np.array(
            [
                self.ds.PixelSpacing[0],
                self.ds.PixelSpacing[1],
                self.ds.GridFrameOffsetVector[1]
                - self.ds.GridFrameOffsetVector[0],
            ]
        )

    @property
    def offset(self):
        """Get the coordinates of the dose grid origin (mm)"""
        return np.array(self.ds.ImagePositionPatient, dtype="float")

    ####################################################
    # Tools
    ####################################################
    def __add__(self, other):
        """Overload + operator to sum this dose grid with the other dose grid

        Parameters
        ----------
        other : DoseGrid
            Another DoseGrid object.
        """
        new = deepcopy(self)
        new.add(other)
        return new

    def __mul__(self, factor):
        """Overload * operator to scale this dose grid by the provided factor

        Parameters
        ----------
        factor : int, float
            Scale the dose grid by this value.
        """
        new = deepcopy(self)
        new.multiply(factor)
        return new

    def __rmul__(self, factor):
        return self.__mul__(factor)

    def multiply(self, factor):
        """
        Scale the dose grid.

        Parameters
        ----------
        factor : int, float
            Multiply the dose grid by this factor.
        """

        if factor < 0:
            raise NotImplementedError("Negative doses are not supported.")

        self.dose_grid *= factor
        self.dose_grid_post_processing()

    def dose_grid_post_processing(self, other=None):
        """Set the pixel data and store UIDs from other DoseGrid"""
        self.set_pixel_data()
        if other is not None:
            self.other_sop_class_uid = other.sop_class_uid
            self.other_sop_instance_uid = other.sop_instance_uid

    def is_coincident(self, other):
        """Check dose grid spatial coincidence.

        Parameters
        ----------
        other : DoseGrid
            Another DoseGrid object.
        """
        return (
            self.ds.PixelSpacing == other.ds.PixelSpacing
            and self.ds.ImagePositionPatient == other.ds.ImagePositionPatient
            and self.ds.pixel_array.shape == other.ds.pixel_array.shape
            and self.ds.GridFrameOffsetVector == other.ds.GridFrameOffsetVector
        )

    def set_pixel_data(self):
        """Update the PixelData with the current dose_grid"""
        self.ds.BitsAllocated = 32
        self.ds.BitsStored = 32
        self.ds.HighBit = 31
        self.ds.DoseGridScaling = (
            np.max(self.dose_grid) / np.iinfo(np.uint32).max
        )
        pixel_data = (
            np.swapaxes(self.dose_grid, 0, 2) / self.ds.DoseGridScaling
        )
        self.ds.PixelData = np.uint32(pixel_data).tobytes()

    def save_dcm(self, file_path):
        """Save the pydicom.FileDataset to file"""
        self.update_dicom_tags()
        self.ds.save_as(file_path)

    def get_ijk_points(self, other_axes):
        """Convert axes from another DoseGrid into ijk of this DoseGrid.

        Parameters
        ----------
        other_axes : list
            The x, y, and z axis arrays.

        Returns
        -------
        np.vstack
            Array of other_axes in this ijk space.
        """
        ijk_axes = [
            (np.array(axis) - self.offset[a]) / self.scale[a]
            for a, axis in enumerate(other_axes)
        ]
        j, i, k = np.meshgrid(ijk_axes[1], ijk_axes[0], ijk_axes[2])
        return np.vstack((i.ravel(), j.ravel(), k.ravel()))

    ####################################################
    # Dose Summation
    ####################################################
    def add(self, other, force=False):
        """
        Add another dose grid to this dose grid, with interpolation if needed

        Parameters
        ----------
        other : DoseGrid
            Another DoseGrid object.
        force : bool
            Set to True to ignore differences in DoseSummationType, DoseType,
            DoseUnits, ImageOrientationPatient
        """

        attrs = [
            "DoseSummationType",
            "DoseType",
            "DoseUnits",
            "ImageOrientationPatient",
        ]
        attr_check = [
            validate_attr_equality(self.ds, other.ds, attr) for attr in attrs
        ]
        if not force and not all(attr_check):
            mismatches = [
                attr for i, attr in enumerate(attrs) if attr_check[i]
            ]
            raise NotImplementedError(
                "Dose summation of dose grids with these mismatched "
                "attributes is not recommended: %s. Use "
                "DoseGrid.add(other, force=True) to ignore"
                % ",".join(mismatches)
            )

        if self.is_coincident(other):
            self.direct_sum(other)
        else:
            if not scipy_available:
                raise ImportError(
                    "scipy must be installed to perform interpolated dose sum."
                )
            self.interp_sum(other)

    def direct_sum(self, other):
        """Directly sum two coincident dose grids

        Parameters
        ----------
        other: DoseGrid
            Another DoseGrid object.
        """
        self.dose_grid += other.dose_grid
        self.summation_type = "DIRECT"

        self.dose_grid_post_processing(other)

    def interp_sum(self, other):
        """
        Interpolate the other dose grid to this dose grid's axes,
        then perform direct summation

        Parameters
        ----------
        other: DoseGrid
            Another DoseGrid object.
        """

        self.dose_grid += self.interp_entire_grid(other)
        self.summation_type = "INTERPOLATED"

        self.dose_grid_post_processing(other)

    def interp_entire_grid(self, other):
        """
        Interpolate the other dose grid to this dose grid's axes in one
        operation

        Parameters
        ----------
        other: DoseGrid
            Another DoseGrid object.

        Returns
        -------
        np.array
            The other dose grid interpolated to this dose grid's axes
        """
        return map_coordinates(
            input=other.dose_grid,
            coordinates=other.get_ijk_points(self.axes),
            order=self.order,
        ).reshape(self.shape)

    def update_dicom_tags(self):
        """Update DICOM UIDs, Content Date/Time, and Dose Comment"""

        # Store the source SOPClassUID and SOPInstanceUID
        seq_data = {
            "ReferencedSOPClassUID": self.sop_class_uid,
            "ReferencedSOPInstanceUID": self.sop_instance_uid,
        }
        add_dicom_sequence(self.ds, "ReferencedInstanceSequence", seq_data)

        if self.other_sop_class_uid is not None:
            seq_data = {
                "ReferencedSOPClassUID": self.other_sop_class_uid,
                "ReferencedSOPInstanceUID": self.other_sop_instance_uid,
            }
            add_dicom_sequence(self.ds, "ReferencedInstanceSequence", seq_data)

        # Create a new SOPInstanceUID
        set_dicom_tag_value(
            self.ds,
            "SOPInstanceUID",
            generate_uid(prefix=dicompyler_uid_prefix_rtdose),
        )

        # Store the dose summation type in the DoseComment tag
        if self.summation_type:
            set_dicom_tag_value(
                self.ds, "DoseComment", "%s SUMMATION" % self.summation_type
            )

        # Update the Date and Time tags
        now = datetime.now()
        set_dicom_tag_value(self.ds, "ContentDate", now.strftime("%Y%m%d"))
        set_dicom_tag_value(self.ds, "ContentTime", now.strftime("%H%M%S"))


def set_dicom_tag_value(ds, tag, value):
    """Set or update a DICOM tag value in the pydicom dataset.

    Parameters
    ----------
    ds : pydicom Dataset
        The pydicom dataset for the tag to be added/updated to.
    tag : str, int or tuple
        DICOM tag or keyword to be added.
    value : any
        New value for the tag's element.
    """
    try:
        ds[tag].value = value
    except KeyError:
        if tag in keyword_dict:  # Keyword provided rather than int or tuple
            tag = keyword_dict[tag]
        ds.add_new(tag, dictionary_VR(tag), value)


def add_dicom_sequence(ds, seq_keyword, data_set_dict):
    """Add a sequence to a data set.

    Parameters
    ----------
    ds : pydicom Dataset
        The pydicom dataset for the sequence to be added to.
    seq_keyword : str
        The DICOM keyword for the sequence.
    data_set_dict : dict
        Dictionary of tags and values for the sequence element.
    """
    seq_ds = Dataset()
    for tag, value in data_set_dict.items():
        set_dicom_tag_value(seq_ds, tag, value)

    if hasattr(ds, seq_keyword):
        getattr(ds, seq_keyword).append(seq_ds)
    else:
        setattr(ds, seq_keyword, Sequence([seq_ds]))


def validate_attr_equality(obj_1, obj_2, attr):
    """Assess the equality of the provided attr between two objects.
    Send warning if unequal.

    Parameters
    ----------
    obj_1 : object
        Any object with an `attr` attribute that is comparable by !=
    obj_2 : object
        Any object with an `attr` attribute that is comparable by !=
    attr : str
        The attribute to be compared between obj_1 and obj_2
    """
    val_1 = getattr(obj_1, attr)
    val_2 = getattr(obj_2, attr)
    if val_1 != val_2:
        warn("Different %s values detected:\n%s\n%s" % (attr, val_1, val_2))
        return False
    return True

1	#!/usr/bin/env python
2	# -- coding: utf-8 --
3	# dose.py
4	"""Routines to access and modify DICOM RT Dose."""	4✔
5	# Copyright (c) 2009-2016 Aditya Panchal
6	# Copyright (c) 2019-2020 Dan Cutright
7	# This file is part of dicompyler-core, released under a BSD license.
8	# See the file license.txt included with this distribution, also
9	# available at https://github.com/dicompyler/dicompyler-core/
10	#
11	# This code was adapted from dicom_dose_sum.py from DVH Analytics:
12	# https://github.com/cutright/DVH-Analytics/
13
14	from copy import deepcopy	4✔
15	import numpy as np	4✔
16	from dicompylercore import dicomparser	4✔
17	from pydicom.uid import generate_uid	4✔
18	from pydicom.datadict import dictionary_VR, keyword_dict	4✔
19	from dicompylercore.config import dicompyler_uid_prefix_rtdose, scipy_available	4✔
20	from datetime import datetime	4✔
21	from pydicom.sequence import Sequence	4✔
22	from pydicom.dataset import Dataset	4✔
23	from warnings import warn	4✔
24
25	if scipy_available:	4!
26	from scipy.ndimage import map_coordinates	4✔
27
28
29	class DoseGrid:	4✔
30	"""
31	Class to easily access commonly used attributes of a DICOM dose grid and
32	make modifications
33
34	Example: Add two dose grids
35	grid_1 = DoseGrid(dose_file_1)
36	grid_2 = DoseGrid(dose_file_2)
37	grid_sum = grid_1 + grid_2
38	grid_sum.save_dcm(some_file_path)
39
40	"""
41
42	def __init__(self, rt_dose, order=1):	4✔
43	""" Initialization of a DoseGrid from a DICOM-RT Dose file or dataset.
44
45	Parameters
46	----------
47	rt_dose : pydicom Dataset or filename
48	DICOM RT Dose used to determine the structure dose grid data.
49	order : int, optional
50	The order of the spline interpolation.
51	0: the nearest grid point, 1: trilinear, 2 to 5: spline
52	"""
53
54	self.ds = dicomparser.DicomParser(rt_dose).ds	4✔
55	self.order = order	4✔
56
57	self.summation_type = None	4✔
58	self.sop_class_uid = self.ds.SOPClassUID	4✔
59	self.sop_instance_uid = self.ds.SOPInstanceUID	4✔
60	self.other_sop_class_uid = None	4✔
61	self.other_sop_instance_uid = None	4✔
62
63	if self.ds.Modality == "RTDOSE":	4✔
64	self.x_axis = (	4✔
65	np.arange(self.ds.Columns) * self.ds.PixelSpacing[0]
66	+ self.ds.ImagePositionPatient[0]
67	)
68	self.y_axis = (	4✔
69	np.arange(self.ds.Rows) * self.ds.PixelSpacing[1]
70	+ self.ds.ImagePositionPatient[1]
71	)
72	self.z_axis = (	4✔
73	np.array(self.ds.GridFrameOffsetVector)
74	+ self.ds.ImagePositionPatient[2]
75	)
76
77	# x and z are swapped in the pixel_array
78	pixel_array = self.ds.pixel_array * self.ds.DoseGridScaling	4✔
79	self.dose_grid = np.swapaxes(pixel_array, 0, 2)	4✔
80	else:
81	raise AttributeError(	4✔
82	"The DoseGrid class requires an RTDOSE file or dataset. "
83	"%s was detected" % self.ds.Modality
84	)
85
86	####################################################
87	# Basic properties
88	####################################################
89	@property	4✔
90	def shape(self):
91	"""Get the x, y, z dimensions of the dose grid"""
92	return (	4✔
93	self.ds.Columns,
94	self.ds.Rows,
95	len(self.ds.GridFrameOffsetVector),
96	)
97
98	@property	4✔
99	def axes(self):
100	"""Get the x, y, z axes of the dose grid (in mm)"""
101	return [self.x_axis, self.y_axis, self.z_axis]	4✔
102
103	@property	4✔
104	def scale(self):
105	"""Get the dose grid resolution (xyz)"""
106	if np.any(np.diff(np.diff(self.ds.GridFrameOffsetVector))):	4!
107	raise NotImplementedError(	×
108	"Non-uniform GridFrameOffsetVector detected. Interpolated "
109	"summation of non-uniform dose-grid scales is not supported."
110	)
111	return np.array(	4✔
112	[
113	self.ds.PixelSpacing[0],
114	self.ds.PixelSpacing[1],
115	self.ds.GridFrameOffsetVector[1]
116	- self.ds.GridFrameOffsetVector[0],
117	]
118	)
119
120	@property	4✔
121	def offset(self):
122	"""Get the coordinates of the dose grid origin (mm)"""
123	return np.array(self.ds.ImagePositionPatient, dtype="float")	4✔
124
125	####################################################
126	# Tools
127	####################################################
128	def __add__(self, other):	4✔
129	"""Overload + operator to sum this dose grid with the other dose grid
130
131	Parameters
132	----------
133	other : DoseGrid
134	Another DoseGrid object.
135	"""
136	new = deepcopy(self)	4✔
137	new.add(other)	4✔
138	return new	4✔
139
140	def __mul__(self, factor):	4✔
141	"""Overload * operator to scale this dose grid by the provided factor
142
143	Parameters
144	----------
145	factor : int, float
146	Scale the dose grid by this value.
147	"""
148	new = deepcopy(self)	4✔
149	new.multiply(factor)	4✔
150	return new	4✔
151
152	def __rmul__(self, factor):	4✔
153	return self.__mul__(factor)	4✔
154
155	def multiply(self, factor):	4✔
156	"""
157	Scale the dose grid.
158
159	Parameters
160	----------
161	factor : int, float
162	Multiply the dose grid by this factor.
163	"""
164
165	if factor < 0:	4!
166	raise NotImplementedError("Negative doses are not supported.")	×
167
168	self.dose_grid *= factor	4✔
169	self.dose_grid_post_processing()	4✔
170
171	def dose_grid_post_processing(self, other=None):	4✔
172	"""Set the pixel data and store UIDs from other DoseGrid"""
173	self.set_pixel_data()	4✔
174	if other is not None:	4✔
175	self.other_sop_class_uid = other.sop_class_uid	4✔
176	self.other_sop_instance_uid = other.sop_instance_uid	4✔
177
178	def is_coincident(self, other):	4✔
179	"""Check dose grid spatial coincidence.
180
181	Parameters
182	----------
183	other : DoseGrid
184	Another DoseGrid object.
185	"""
186	return (	4✔
187	self.ds.PixelSpacing == other.ds.PixelSpacing
188	and self.ds.ImagePositionPatient == other.ds.ImagePositionPatient
189	and self.ds.pixel_array.shape == other.ds.pixel_array.shape
190	and self.ds.GridFrameOffsetVector == other.ds.GridFrameOffsetVector
191	)
192
193	def set_pixel_data(self):	4✔
194	"""Update the PixelData with the current dose_grid"""
195	self.ds.BitsAllocated = 32	4✔
196	self.ds.BitsStored = 32	4✔
197	self.ds.HighBit = 31	4✔
198	self.ds.DoseGridScaling = (	4✔
199	np.max(self.dose_grid) / np.iinfo(np.uint32).max
200	)
201	pixel_data = (	4✔
202	np.swapaxes(self.dose_grid, 0, 2) / self.ds.DoseGridScaling
203	)
204	self.ds.PixelData = np.uint32(pixel_data).tobytes()	4✔
205
206	def save_dcm(self, file_path):	4✔
207	"""Save the pydicom.FileDataset to file"""
208	self.update_dicom_tags()	4✔
209	self.ds.save_as(file_path)	4✔
210
211	def get_ijk_points(self, other_axes):	4✔
212	"""Convert axes from another DoseGrid into ijk of this DoseGrid.
213
214	Parameters
215	----------
216	other_axes : list
217	The x, y, and z axis arrays.
218
219	Returns
220	-------
221	np.vstack
222	Array of other_axes in this ijk space.
223	"""
224	ijk_axes = [	4✔
225	(np.array(axis) - self.offset[a]) / self.scale[a]
226	for a, axis in enumerate(other_axes)
227	]
228	j, i, k = np.meshgrid(ijk_axes[1], ijk_axes[0], ijk_axes[2])	4✔
229	return np.vstack((i.ravel(), j.ravel(), k.ravel()))	4✔
230
231	####################################################
232	# Dose Summation
233	####################################################
234	def add(self, other, force=False):	4✔
235	"""
236	Add another dose grid to this dose grid, with interpolation if needed
237
238	Parameters
239	----------
240	other : DoseGrid
241	Another DoseGrid object.
242	force : bool
243	Set to True to ignore differences in DoseSummationType, DoseType,
244	DoseUnits, ImageOrientationPatient
245	"""
246
247	attrs = [	4✔
248	"DoseSummationType",
249	"DoseType",
250	"DoseUnits",
251	"ImageOrientationPatient",
252	]
253	attr_check = [	4✔
254	validate_attr_equality(self.ds, other.ds, attr) for attr in attrs
255	]
256	if not force and not all(attr_check):	4✔
257	mismatches = [	4✔
258	attr for i, attr in enumerate(attrs) if attr_check[i]
259	]
260	raise NotImplementedError(	4✔
261	"Dose summation of dose grids with these mismatched "
262	"attributes is not recommended: %s. Use "
263	"DoseGrid.add(other, force=True) to ignore"
264	% ",".join(mismatches)
265	)
266
267	if self.is_coincident(other):	4!
268	self.direct_sum(other)	4✔
269	else:
270	if not scipy_available:	×
271	raise ImportError(	×
272	"scipy must be installed to perform interpolated dose sum."
273	)
274	self.interp_sum(other)	×
275
276	def direct_sum(self, other):	4✔
277	"""Directly sum two coincident dose grids
278
279	Parameters
280	----------
281	other: DoseGrid
282	Another DoseGrid object.
283	"""
284	self.dose_grid += other.dose_grid	4✔
285	self.summation_type = "DIRECT"	4✔
286
287	self.dose_grid_post_processing(other)	4✔
288
289	def interp_sum(self, other):	4✔
290	"""
291	Interpolate the other dose grid to this dose grid's axes,
292	then perform direct summation
293
294	Parameters
295	----------
296	other: DoseGrid
297	Another DoseGrid object.
298	"""
299
300	self.dose_grid += self.interp_entire_grid(other)	4✔
301	self.summation_type = "INTERPOLATED"	4✔
302
303	self.dose_grid_post_processing(other)	4✔
304
305	def interp_entire_grid(self, other):	4✔
306	"""
307	Interpolate the other dose grid to this dose grid's axes in one
308	operation
309
310	Parameters
311	----------
312	other: DoseGrid
313	Another DoseGrid object.
314
315	Returns
316	-------
317	np.array
318	The other dose grid interpolated to this dose grid's axes
319	"""
320	return map_coordinates(	4✔
321	input=other.dose_grid,
322	coordinates=other.get_ijk_points(self.axes),
323	order=self.order,
324	).reshape(self.shape)
325
326	def update_dicom_tags(self):	4✔
327	"""Update DICOM UIDs, Content Date/Time, and Dose Comment"""
328
329	# Store the source SOPClassUID and SOPInstanceUID
330	seq_data = {	4✔
331	"ReferencedSOPClassUID": self.sop_class_uid,
332	"ReferencedSOPInstanceUID": self.sop_instance_uid,
333	}
334	add_dicom_sequence(self.ds, "ReferencedInstanceSequence", seq_data)	4✔
335
336	if self.other_sop_class_uid is not None:	4!
337	seq_data = {	×
338	"ReferencedSOPClassUID": self.other_sop_class_uid,
339	"ReferencedSOPInstanceUID": self.other_sop_instance_uid,
340	}
341	add_dicom_sequence(self.ds, "ReferencedInstanceSequence", seq_data)	×
342
343	# Create a new SOPInstanceUID
344	set_dicom_tag_value(	4✔
345	self.ds,
346	"SOPInstanceUID",
347	generate_uid(prefix=dicompyler_uid_prefix_rtdose),
348	)
349
350	# Store the dose summation type in the DoseComment tag
351	if self.summation_type:	4!
352	set_dicom_tag_value(	×
353	self.ds, "DoseComment", "%s SUMMATION" % self.summation_type
354	)
355
356	# Update the Date and Time tags
357	now = datetime.now()	4✔
358	set_dicom_tag_value(self.ds, "ContentDate", now.strftime("%Y%m%d"))	4✔
359	set_dicom_tag_value(self.ds, "ContentTime", now.strftime("%H%M%S"))	4✔
360
361
362	def set_dicom_tag_value(ds, tag, value):	4✔
363	"""Set or update a DICOM tag value in the pydicom dataset.
364
365	Parameters
366	----------
367	ds : pydicom Dataset
368	The pydicom dataset for the tag to be added/updated to.
369	tag : str, int or tuple
370	DICOM tag or keyword to be added.
371	value : any
372	New value for the tag's element.
373	"""
374	try:	4✔
375	ds[tag].value = value	4✔
376	except KeyError:	4✔
377	if tag in keyword_dict: # Keyword provided rather than int or tuple	4!
378	tag = keyword_dict[tag]	4✔
379	ds.add_new(tag, dictionary_VR(tag), value)	4✔
380
381
382	def add_dicom_sequence(ds, seq_keyword, data_set_dict):	4✔
383	"""Add a sequence to a data set.
384
385	Parameters
386	----------
387	ds : pydicom Dataset
388	The pydicom dataset for the sequence to be added to.
389	seq_keyword : str
390	The DICOM keyword for the sequence.
391	data_set_dict : dict
392	Dictionary of tags and values for the sequence element.
393	"""
394	seq_ds = Dataset()	4✔
395	for tag, value in data_set_dict.items():	4✔
396	set_dicom_tag_value(seq_ds, tag, value)	4✔
397
398	if hasattr(ds, seq_keyword):	4✔
399	getattr(ds, seq_keyword).append(seq_ds)	4✔
400	else:
401	setattr(ds, seq_keyword, Sequence([seq_ds]))	4✔
402
403
404	def validate_attr_equality(obj_1, obj_2, attr):	4✔
405	"""Assess the equality of the provided attr between two objects.
406	Send warning if unequal.
407
408	Parameters
409	----------
410	obj_1 : object
411	Any object with an `attr` attribute that is comparable by !=
412	obj_2 : object
413	Any object with an `attr` attribute that is comparable by !=
414	attr : str
415	The attribute to be compared between obj_1 and obj_2
416	"""
417	val_1 = getattr(obj_1, attr)	4✔
418	val_2 = getattr(obj_2, attr)	4✔
419	if val_1 != val_2:	4✔
420	warn("Different %s values detected:\n%s\n%s" % (attr, val_1, val_2))	4✔
421	return False	4✔
422	return True	4✔

dicompyler / dicompyler-core / 799

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