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test_util.py
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test_util.py
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# Copyright 2008-2021 pydicom authors. See LICENSE file for details.
"""Test suite for util functions"""
import copy
from contextlib import contextmanager
import pytest
from pydicom import config, dcmread, Dataset, Sequence
from pydicom import filereader
from pydicom._private_dict import private_dictionaries
from pydicom.data import get_testdata_file
from pydicom.dataelem import DataElement
from pydicom.tag import Tag
from pydicom.uid import (
ImplicitVRLittleEndian, ExplicitVRBigEndian, ExplicitVRLittleEndian
)
from pydicom.util import fixer
from pydicom.util import hexutil
from pydicom.util.codify import (
camel_to_underscore,
tag_repr,
default_name_filter,
code_imports,
code_dataelem,
code_dataset,
main as codify_main,
)
from pydicom.util.dump import *
from pydicom.util.hexutil import hex2bytes, bytes2hex
from pydicom.util.leanread import dicomfile
have_numpy = True
try:
import numpy
except ImportError:
have_numpy = False
test_dir = os.path.dirname(__file__)
raw_hex_module = os.path.join(test_dir, '_write_stds.py')
raw_hex_code = open(raw_hex_module, "rb").read()
class TestCodify:
"""Test the utils.codify module"""
def test_camel_to_underscore(self):
"""Test utils.codify.camel_to_underscore"""
input_str = ['TheNameToConvert', 'Some12Variable_Name']
output_str = ['the_name_to_convert', 'some12_variable__name']
for in_str, out_str in zip(input_str, output_str):
assert out_str == camel_to_underscore(in_str)
def test_tag_repr(self):
"""Test utils.codify.tag_repr"""
input_tag = [0x00000000, 0x00100010, 0x7fe00010, 0x11110001]
output_str = ['(0x0000, 0x0000)', '(0x0010, 0x0010)',
'(0x7fe0, 0x0010)', '(0x1111, 0x0001)']
for tag, out_str in zip(input_tag, output_str):
assert out_str == tag_repr(Tag(tag))
def test_default_name_filter(self):
"""Test utils.codify.default_name_filter"""
input_keyword = ['ControlPointSet', 'ReferenceDataSet',
'FractionGroupThing']
output_str = ['cp_set', 'ref_data_set', 'frxn_gp_thing']
for in_str, out_str in zip(input_keyword, output_str):
assert out_str == default_name_filter(in_str)
def test_code_imports(self):
"""Test utils.codify.code_imports"""
out = 'import pydicom\n'
out += 'from pydicom.dataset import Dataset, FileMetaDataset\n'
out += 'from pydicom.sequence import Sequence'
assert out == code_imports()
def test_code_dataelem_standard(self):
"""Test utils.codify.code_dataelem for standard element"""
# Element keyword in data dictionary
input_elem = [DataElement(0x00100010, 'PN', 'CITIZEN'),
DataElement(0x0008010c, 'UI', '1.1.2.3.4.5'),
DataElement(0x00080301, 'US', 1200)]
out_str = ["ds.PatientName = 'CITIZEN'",
"ds.CodingSchemeUID = '1.1.2.3.4.5'",
"ds.PrivateGroupReference = 1200"]
for elem, out in zip(input_elem, out_str):
assert out == code_dataelem(elem)
def test_code_dataelem_exclude_size(self):
"""Test utils.codify.code_dataelem exclude_size param"""
input_elem = [DataElement(0x00100010, 'OB', 'CITIZEN'),
DataElement(0x0008010c, 'UI', '1.1'),
DataElement(0x00200011, 'IS', 3)]
# Fails
# DataElement(0x00080301, 'US', 1200)]
out_str = ["ds.PatientName = # XXX Array of 7 bytes excluded",
"ds.CodingSchemeUID = '1.1'",
"ds.SeriesNumber = '3'"]
# Fails
# "ds.PrivateGroupReference = 1200"]
for elem, out in zip(input_elem, out_str):
assert out == code_dataelem(elem, exclude_size=4)
def test_code_dataelem_private(self):
"""Test utils.codify.code_dataelem"""
# Element keyword not in data dictionary
input_elem = [DataElement(0x00111010, 'PN', 'CITIZEN'),
DataElement(0x0081010c, 'UI', '1.1.2.3.4.5'),
DataElement(0x11110301, 'US', 1200)]
out_str = ["ds.add_new((0x0011, 0x1010), 'PN', 'CITIZEN')",
"ds.add_new((0x0081, 0x010c), 'UI', '1.1.2.3.4.5')",
"ds.add_new((0x1111, 0x0301), 'US', 1200)"]
for elem, out in zip(input_elem, out_str):
assert out == code_dataelem(elem)
def test_code_dataelem_sequence(self):
"""Test utils.codify.code_dataelem"""
# ControlPointSequence
elem = DataElement(0x300A0111, 'SQ', [])
out = "\n# Control Point Sequence\n"
out += "cp_sequence = Sequence()\n"
out += "ds.ControlPointSequence = cp_sequence"
assert out == code_dataelem(elem)
def test_code_sequence(self):
"""Test utils.codify.code_dataelem"""
# ControlPointSequence
elem = DataElement(0x300A0111, 'SQ', [])
elem.value.append(Dataset())
elem.value[0].PatientID = '1234'
out = (
"\n"
"# Control Point Sequence\n"
"cp_sequence = Sequence()\n"
"ds.ControlPointSequence = cp_sequence\n"
"\n"
"# Control Point Sequence: Control Point 1\n"
"cp1 = Dataset()\n"
"cp_sequence.append(cp1)\n"
"cp1.PatientID = '1234'"
)
assert out == code_dataelem(elem)
def test_codify_recurring_keyword(self):
"""Test utils.codify.code_dataset with same keyword nested"""
# Create fake Dataset with repeated DICOM keyword nested
# (0040, a730) Content Sequence 1 item(s) ----
# (0040, a040) Value Type CS: 'CODE'
# (0040, a730) Content Sequence 1 item(s) ----
# (0040, a040) Value Type CS: 'CODE'
ds = Dataset()
ds.ContentSequence = seq1 = Sequence()
seq1.append(Dataset())
seq1[0].ValueType = "CODE"
seq1[0].ContentSequence = seq2 = Sequence()
seq2.append(Dataset())
seq2[0].ValueType = "CODE_1"
ds_code = code_dataset(ds)
# normal 1st use of var name
assert "content1.ValueType = 'CODE'" in ds_code
# Nested item of same name should have subscript
assert "content1_1.ValueType = 'CODE_1'" in ds_code
def test_code_file(self, capsys):
"""Test utils.codify.code_file"""
filename = get_testdata_file("rtplan.dcm")
args = ["--save-as", r"c:\temp\testout.dcm", filename]
codify_main(100, args)
out, err = capsys.readouterr()
assert r"c:\temp\testout.dcm" in out
def test_code_relative_filename(self, capsys):
"""Test utils.codify.code_file with a relative path that doesn't exist"""
# regression test for #1865
args = ["XXxUN_sequenceXX.dcm"] # file that doesn't exist
with pytest.raises(SystemExit):
codify_main(100, args)
def test_code_dataelem_at(self):
"""Test utils.codify.code_dataelem"""
elem = DataElement(0x00000901, 'AT', (0x1234, 0x5678))
out = 'ds.OffendingElement = (0x1234, 0x5678)'
assert out == code_dataelem(elem)
class TestDump:
"""Test the utils.dump module"""
def test_print_character(self):
"""Test utils.dump.print_character"""
assert print_character(0x30) == '0'
assert print_character(0x31) == '1'
assert print_character(0x39) == '9'
assert print_character(0x41) == 'A'
assert print_character(0x5A) == 'Z'
assert print_character(0x61) == 'a'
assert print_character(0x7A) == 'z'
assert print_character(0x00) == '.'
def test_filedump(self):
"""Test utils.dump.filedump"""
p = get_testdata_file("CT_small.dcm")
s = filedump(p, start_address=500, stop_address=1000)
assert (
"000 49 49 2A 00 54 18 08 00 00 00 00 00 00 00 00 00 "
"II*.T..........."
) not in s
assert (
"1F4 2E 31 2E 31 2E 31 2E 31 2E 32 30 30 34 30 31 31 "
".1.1.1.1.2004011"
) in s
def test_datadump(self):
"""Test utils.dump.datadump"""
p = get_testdata_file("CT_small.dcm")
with open(p, 'rb') as f:
s = datadump(f.read(), 500, 1000)
assert (
"1F4 2E 31 2E 31 2E 31 2E 31 2E 32 30 30 34 30 31 31 "
".1.1.1.1.2004011"
) in s
def test_hexdump(self):
"""Test utils.dump.hexdump"""
# Default
p = get_testdata_file("CT_small.dcm")
with open(p, 'rb') as f:
s = hexdump(f)
assert (
"0000 49 49 2A 00 54 18 08 00 00 00 00 00 00 00 00 00 "
"II*.T..........."
) in s
assert (
"0170 41 4C 5C 50 52 49 4D 41 52 59 5C 41 58 49 41 4C "
"AL.PRIMARY.AXIAL"
) in s
assert (
"9920 08 00 00 00 00 00 ......"
) in s
# `stop_address` parameter
with open(p, 'rb') as f:
s = hexdump(f, stop_address=1000)
assert (
"000 49 49 2A 00 54 18 08 00 00 00 00 00 00 00 00 00 "
"II*.T..........."
) in s
assert (
"170 41 4C 5C 50 52 49 4D 41 52 59 5C 41 58 49 41 4C "
"AL.PRIMARY.AXIAL"
) in s
assert (
"9920 08 00 00 00 00 00 ......"
) not in s
# `show_address` parameter
with open(p, 'rb') as f:
s = hexdump(f, show_address=False, stop_address=1000)
assert (
"49 49 2A 00 54 18 08 00 00 00 00 00 00 00 00 00 "
"II*.T..........."
) in s
assert (
"000 49 49 2A 00 54 18 08 00 00 00 00 00 00 00 00 00 "
"II*.T..........."
) not in s
# `start_address` parameter
with open(p, 'rb') as f:
s = hexdump(f, start_address=500, stop_address=1000)
assert (
"000 49 49 2A 00 54 18 08 00 00 00 00 00 00 00 00 00 "
"II*.T..........."
) not in s
assert (
"1F4 2E 31 2E 31 2E 31 2E 31 2E 32 30 30 34 30 31 31 "
".1.1.1.1.2004011"
) in s
def test_pretty_print(self, capsys):
"""Test utils.dump.pretty_print"""
ds = get_testdata_file("CT_small.dcm", read=True)
pretty_print(ds)
s = capsys.readouterr().out
assert (
"(0008, 0005) Specific Character Set CS: 'ISO_IR 100'"
) in s
assert (
"(0010, 1002) Other Patient IDs Sequence -- 2 item(s)"
) in s
assert (
" (0010, 0022) Type of Patient ID CS: 'TEXT'"
) in s
assert (
"(fffc, fffc) Data Set Trailing Padding OB: Array of "
"126 elements"
) in s
class TestFixer:
"""Test the utils.fixer module"""
def test_fix_separator_callback(self):
"""Test utils.fixer.fix_separator_callback"""
pass
def test_fix_separator(self):
"""Test utils.fixer.fix_separator"""
pass
def test_mismatch_callback(self):
"""Test utils.fixer.mismatch_callback"""
pass
def test_fix_mismatch(self):
"""Test utils.fixer.fix_mismatch"""
pass
class TestHexUtil:
"""Test the utils.hexutil module"""
def test_hex_to_bytes(self):
"""Test utils.hexutil.hex2bytes"""
hexstring = "00 01 02 03 04 05 06 07 08 09 0A 0B 0C 0D 0E 0F"
bytestring = (
b'\x00\x01\x02\x03\x04\x05\x06\x07\x08\x09'
b'\x0A\x0B\x0C\x0D\x0E\x0F'
)
assert hex2bytes(hexstring) == bytestring
hexstring = "00 10 20 30 40 50 60 70 80 90 A0 B0 C0 D0 E0 F0"
bytestring = (
b'\x00\x10\x20\x30\x40\x50\x60\x70\x80\x90'
b'\xA0\xB0\xC0\xD0\xE0\xF0'
)
assert hex2bytes(hexstring) == bytestring
hexstring = b"00 01 02 03 04 05 06 07 08 09 0A 0B 0C 0D 0E 0F"
bytestring = (
b'\x00\x01\x02\x03\x04\x05\x06\x07\x08\x09'
b'\x0A\x0B\x0C\x0D\x0E\x0F'
)
assert hex2bytes(hexstring) == bytestring
with pytest.raises(TypeError):
hex2bytes(0x1234)
def test_bytes_to_hex(self):
"""Test utils.hexutil.hex2bytes"""
hexstring = "00 01 02 03 04 05 06 07 08 09 0a 0b 0c 0d 0e 0f"
bytestring = (
b'\x00\x01\x02\x03\x04\x05\x06\x07\x08\x09'
b'\x0A\x0B\x0C\x0D\x0E\x0F'
)
assert bytes2hex(bytestring) == hexstring
hexstring = "00 10 20 30 40 50 60 70 80 90 a0 b0 c0 d0 e0 f0"
bytestring = (
b'\x00\x10\x20\x30\x40\x50\x60\x70\x80\x90'
b'\xA0\xB0\xC0\xD0\xE0\xF0'
)
assert bytes2hex(bytestring) == hexstring
class TestDataElementCallbackTests:
def setup_method(self):
# Set up a dataset with commas in one item instead of backslash
namespace = {}
exec(raw_hex_code, {}, namespace)
ds_bytes = hexutil.hex2bytes(namespace['impl_LE_deflen_std_hex'])
# Change "2\4\8\16" to "2,4,8,16"
ds_bytes = ds_bytes.replace(b"\x32\x5c\x34\x5c\x38\x5c\x31\x36",
b"\x32\x2c\x34\x2c\x38\x2c\x31\x36")
self.ds_bytes = ds_bytes
self.bytesio = BytesIO(ds_bytes)
def teardown_method(self):
config.reset_data_element_callback()
def test_bad_separator(self, enforce_valid_values):
"""Ensure that unchanged bad separator does raise an error..."""
ds = filereader.read_dataset(self.bytesio, is_little_endian=True,
is_implicit_VR=True)
contour = ds.ROIContourSequence[0].ContourSequence[0]
with pytest.raises(ValueError):
getattr(contour, "ContourData")
def test_impl_vr_comma(self):
"""util.fix_separator:
Able to replace comma in Implicit VR dataset.."""
fixer.fix_separator(b",", for_VRs=["DS", "IS"],
process_unknown_VRs=False)
ds = filereader.read_dataset(self.bytesio, is_little_endian=True,
is_implicit_VR=True)
got = ds.ROIContourSequence[0].ContourSequence[0].ContourData
expected = [2., 4., 8., 16.]
if have_numpy and config.use_DS_numpy:
assert numpy.allclose(expected, got)
else:
assert expected == got
def test_null_value_for_fixed_vr(self):
# Wipe first Contour Data, mark as length 0
null_ds_bytes = self.ds_bytes.replace(b"\x08\x00\x00\x00",
b"\x00\x00\x00\x00")
contour_data = b"\x32\x2c\x34\x2c\x38\x2c\x31\x36"
null_ds_bytes = null_ds_bytes.replace(contour_data, b"")
fixer.fix_separator(b",", for_VRs=["DS", "IS"],
process_unknown_VRs=False)
ds = filereader.read_dataset(BytesIO(null_ds_bytes),
is_little_endian=True,
is_implicit_VR=True)
assert ds.ROIContourSequence[0].ContourSequence[0].ContourData is None
def test_space_delimiter(self):
# Change "32\64\128\196" to "32 64 128 196", keeping the trailing space
existing = b"\x33\x32\x5c\x36\x34\x5c\x31\x32\x38\x5c\x31\x39\x36\x20"
spaced = b"\x33\x32\x20\x36\x34\x20\x31\x32\x38\x20\x31\x39\x36\x20"
space_ds_bytes = self.ds_bytes.replace(existing, spaced)
fixer.fix_separator(b" ", for_VRs=["DS", "IS"],
process_unknown_VRs=False)
ds = filereader.read_dataset(BytesIO(space_ds_bytes),
is_little_endian=True,
is_implicit_VR=True)
got = ds.ROIContourSequence[0].ContourSequence[1].ContourData
expected = [32., 64., 128., 196.]
if have_numpy and config.use_DS_numpy:
assert numpy.allclose(expected, got)
else:
assert expected == got
@pytest.mark.filterwarnings("ignore:Unknown DICOM tag")
def test_process_unknown_vr(self):
bad_vr_bytes = self.ds_bytes
# tag (0900, 0010), length 4, value "1,2"
bad_vr_bytes += (b"\x00\x09\x10\x00"
b"\x04\x00\x00\x00"
b"\x31\x2c\x32\x20")
fixer.fix_separator(b",", for_VRs=["DS", "IS"],
process_unknown_VRs=True)
ds = filereader.read_dataset(BytesIO(bad_vr_bytes),
is_little_endian=True,
is_implicit_VR=True)
got = ds.get((0x0900, 0x0010))
assert got.value == b'1\\2 '
# with process_unknown_VRs=False, unknown VR separator is not replaced
fixer.fix_separator(b",", for_VRs=["DS", "IS"],
process_unknown_VRs=False)
ds = filereader.read_dataset(BytesIO(bad_vr_bytes),
is_little_endian=True,
is_implicit_VR=True)
got = ds.get((0x0900, 0x0010))
assert got.value == b'1,2 '
class TestLeanRead:
def test_explicit_little(self):
p = get_testdata_file("CT_small.dcm")
ds = dcmread(p)
assert ds.file_meta.TransferSyntaxUID == ExplicitVRLittleEndian
with dicomfile(p) as ds:
assert ds.preamble is not None
for elem in ds:
if elem[0] == (0x7fe0, 0x0010):
assert elem[2] == 32768
def test_implicit_little(self):
p = get_testdata_file("MR_small_implicit.dcm")
ds = dcmread(p)
assert ds.file_meta.TransferSyntaxUID == ImplicitVRLittleEndian
with dicomfile(p) as ds:
assert ds.preamble is not None
for elem in ds:
if elem[0] == (0x7fe0, 0x0010):
assert elem[2] == 8192
def test_explicit_big(self):
p = get_testdata_file("MR_small_bigendian.dcm")
ds = dcmread(p)
assert ds.file_meta.TransferSyntaxUID == ExplicitVRBigEndian
with dicomfile(p) as ds:
assert ds.preamble is not None
for elem in ds:
if elem[0] == (0x7fe0, 0x0010):
assert elem[2] == 8192
def test_no_tsyntax(self):
p = get_testdata_file("meta_missing_tsyntax.dcm")
ds = dcmread(p)
assert "TransferSyntaxUID" not in ds.file_meta
msg = "No transfer syntax in file meta info"
with dicomfile(p) as ds:
assert ds.preamble is not None
with pytest.raises(NotImplementedError, match=msg):
for elem in ds:
pass
def test_no_meta(self):
p = get_testdata_file("no_meta.dcm")
msg = "No transfer syntax in file meta info"
with dicomfile(p) as ds:
assert ds.preamble is None
with pytest.raises(NotImplementedError, match=msg):
for elem in ds:
pass
def test_UN_sequence(self):
p = get_testdata_file("UN_sequence.dcm")
msg = "This reader does not handle undefined length except for SQ"
with dicomfile(p) as ds:
with pytest.raises(NotImplementedError, match=msg):
for elem in ds:
pass
@contextmanager
def save_private_dict():
saved_private_dict = copy.deepcopy(private_dictionaries)
try:
yield
finally:
private_dictionaries.clear()
private_dictionaries.update(saved_private_dict)