def test_create_rtss(test_object):
"""
Test for creating an RT Struct file if one does not exist.
:param test_object: test_object function, for accessing the shared
TestIso2Roi object.
"""
# Create file path
file_path = test_object.patient_dict_container.filepaths.values()
file_path = Path(os.path.commonpath(file_path))
file_path = str(file_path.joinpath("rtss.dcm"))
# Get CT UID list
ct_uid_list = ImageLoading.get_image_uid_list(
test_object.patient_dict_container.dataset)
# Generate RTSS
rtss = ROI.create_initial_rtss_from_ct(
test_object.patient_dict_container.dataset[0], file_path, ct_uid_list)
# Get test dataset
test_ds = test_object.patient_dict_container.dataset[0]
# Assert that the ds exists and is not empty
assert rtss
# Assert that certain values are correct
assert rtss.PatientName == test_ds.PatientName
assert rtss.PatientID == test_ds.PatientID
assert rtss.PatientBirthDate == test_ds.PatientBirthDate
assert rtss.PatientSex == test_ds.PatientSex
assert rtss.StudyInstanceUID == test_ds.StudyInstanceUID
assert rtss.Modality == 'RTSTRUCT'
assert rtss.SOPClassUID == '1.2.840.10008.5.1.4.1.1.481.3'
def test_create_initial_rtss_from_ct(qtbot, test_object, init_config):
# Create a test rtss
path = test_object.patient_dict_container.path
rtss_path = Path(path).joinpath('rtss.dcm')
uid_list = ImageLoading.get_image_uid_list(
test_object.patient_dict_container.dataset)
rtss = create_initial_rtss_from_ct(
test_object.patient_dict_container.dataset[1], rtss_path, uid_list)
# type 1 tags - must exist and not be empty
type_1_tags: list = [Tag("StudyInstanceUID"),
Tag("Modality"),
Tag("SeriesInstanceUID"),
Tag("StructureSetLabel"),
Tag("SOPClassUID"),
Tag("SOPInstanceUID")
]
# type 2 tags - must exist and be at least an empty string
type_2_tags: list = [Tag("PatientName"),
Tag("PatientBirthDate"),
Tag("PatientSex"),
Tag("StudyDate"),
Tag("StudyTime"),
Tag("AccessionNumber"),
Tag("ReferringPhysicianName"),
Tag("StudyID"),
Tag("OperatorsName"),
Tag("SeriesNumber"),
Tag("Manufacturer"),
Tag("StructureSetDate"),
Tag("StructureSetTime")
]
# type 1 sequence tags - must exist
type_1_sequence_tags: list = [Tag("StructureSetROISequence"),
Tag("ROIContourSequence"),
Tag("RTROIObservationsSequence")
]
# Checking type 1 tags
for tag in type_1_tags:
assert (tag in rtss) is True
assert rtss[tag].is_empty is False
# Checking type 2 tags
for tag in type_2_tags:
assert (tag in rtss) is True
if rtss[tag].value != "":
assert rtss[tag].is_empty is False
# Checking type 1 sequence tags
for tag in type_1_sequence_tags:
assert (tag in rtss) is True
def create_new_rtstruct(cls, progress_callback):
"""
Generates a new RTSS and edits the patient dict container. Used
for batch processing.
"""
# Get common directory
patient_dict_container = PatientDictContainer()
file_path = patient_dict_container.filepaths.values()
file_path = Path(os.path.commonpath(file_path))
# Get new RT Struct file path
file_path = str(file_path.joinpath("rtss.dcm"))
# Create RT Struct file
progress_callback.emit(("Generating RT Structure Set", 60))
ct_uid_list = ImageLoading.get_image_uid_list(
patient_dict_container.dataset)
ds = ROI.create_initial_rtss_from_ct(patient_dict_container.dataset[0],
file_path, ct_uid_list)
ds.save_as(file_path)
# Add RT Struct file path to patient dict container
patient_dict_container.filepaths['rtss'] = file_path
filepaths = patient_dict_container.filepaths
# Add RT Struct dataset to patient dict container
patient_dict_container.dataset['rtss'] = ds
dataset = patient_dict_container.dataset
# Set some patient dict container attributes
patient_dict_container.set("file_rtss", filepaths['rtss'])
patient_dict_container.set("dataset_rtss", dataset['rtss'])
dicom_tree_rtss = DicomTree(filepaths['rtss'])
patient_dict_container.set("dict_dicom_tree_rtss",
dicom_tree_rtss.dict)
dict_pixluts = ImageLoading.get_pixluts(patient_dict_container.dataset)
patient_dict_container.set("pixluts", dict_pixluts)
rois = ImageLoading.get_roi_info(ds)
patient_dict_container.set("rois", rois)
patient_dict_container.set("selected_rois", [])
patient_dict_container.set("dict_polygons_axial", {})
patient_dict_container.set("rtss_modified", True)
def load_temp_rtss(self, path, progress_callback, interrupt_flag):
"""
Generate a temporary rtss and load its data into
MovingDictContainer
:param path: str. The common root folder of all DICOM files.
:param progress_callback: A signal that receives the current
progress of the loading.
:param interrupt_flag: A threading.Event() object that tells the
function to stop loading.
"""
progress_callback.emit(("Generating temporary rtss...", 20))
moving_dict_container = MovingDictContainer()
rtss_path = Path(path).joinpath('rtss.dcm')
uid_list = ImageLoading.get_image_uid_list(
moving_dict_container.dataset)
rtss = create_initial_rtss_from_ct(moving_dict_container.dataset[0],
rtss_path, uid_list)
if interrupt_flag.is_set(): # Stop loading.
print("stopped")
return False
progress_callback.emit(("Loading temporary rtss...", 50))
# Set ROIs
rois = ImageLoading.get_roi_info(rtss)
moving_dict_container.set("rois", rois)
# Set pixluts
dict_pixluts = ImageLoading.get_pixluts(moving_dict_container.dataset)
moving_dict_container.set("pixluts", dict_pixluts)
# Add RT Struct file path and dataset to moving dict container
moving_dict_container.filepaths['rtss'] = rtss_path
moving_dict_container.dataset['rtss'] = rtss
# Set some moving dict container attributes
moving_dict_container.set("file_rtss", rtss_path)
moving_dict_container.set("dataset_rtss", rtss)
ordered_dict = DicomTree(None).dataset_to_dict(rtss)
moving_dict_container.set("dict_dicom_tree_rtss", ordered_dict)
moving_dict_container.set("selected_rois", [])
def test_merge_rtss(qtbot, test_object):
"""Test merging rtss. This function creates a new rtss, then merges
the new rtss with the old rtss and asserts that duplicated ROIs
will be overwritten when the other being merged.
:param test_object: test_object function, for accessing the shared
TestStructureTab object.
"""
patient_dict_container = PatientDictContainer()
# Create a new rtss
dataset = patient_dict_container.dataset[0]
rtss_path = Path(patient_dict_container.path).joinpath('rtss.dcm')
new_rtss = create_initial_rtss_from_ct(
dataset, rtss_path,
ImageLoading.get_image_uid_list(patient_dict_container.dataset))
# Set ROIs
rois = ImageLoading.get_roi_info(new_rtss)
patient_dict_container.set("rois", rois)
# Add a new ROI into the new rtss with the name of the first ROI in
# the old rtss
roi_name = test_object.rois.get(1)["name"]
roi_coordinates = [0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0]
new_rtss = create_roi(new_rtss, roi_name, [{
'coords': roi_coordinates,
'ds': dataset
}])
# Add a new ROI with a new name
roi_name = "NewTestROI"
new_rtss = create_roi(new_rtss, roi_name, [{
'coords': roi_coordinates,
'ds': dataset
}])
# Set ROIs
rois = ImageLoading.get_roi_info(new_rtss)
patient_dict_container.set("rois", rois)
patient_dict_container.set("existing_file_rtss",
patient_dict_container.get("file_rtss"))
patient_dict_container.set("dataset_rtss", new_rtss)
# Merge the old and new rtss
structure_tab = StructureTab()
structure_tab.show_modified_indicator()
qtbot.addWidget(structure_tab)
def test_message_window():
messagebox = structure_tab.findChild(QtWidgets.QMessageBox)
assert messagebox is not None
yes_button = messagebox.buttons()[1]
qtbot.mouseClick(yes_button, QtCore.Qt.LeftButton, delay=1)
QtCore.QTimer.singleShot(1000, test_message_window)
structure_tab.save_new_rtss_to_fixed_image_set(auto=True)
merged_rtss = pydicom.read_file(patient_dict_container.get("file_rtss"))
merged_rois = ImageLoading.get_roi_info(merged_rtss)
assert (len(test_object.rois) + 1 == len(merged_rois))
