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test_mcd_parser.py
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from pathlib import Path
import pytest
from readimc import MCDFile, MCDParser
class TestMCDParser:
damond_mcd_file_path = Path("data/Damond2019/20170814_G_SE.mcd")
@classmethod
def setup_class(cls):
if cls.damond_mcd_file_path.exists():
cls.damond_mcd_file = MCDFile(cls.damond_mcd_file_path)
cls.damond_mcd_file.open()
else:
cls.damond_mcd_file = None
@classmethod
def teardown_class(cls):
if cls.damond_mcd_file is not None:
cls.damond_mcd_file.close()
cls.damond_mcd_file = None
def test_schema_xml(self):
pass # TODO
def test_schema_xml_elem(self):
pass # TODO
def test_schema_xml_xmlns(self):
pass # TODO
def test_parse_slides(self, imc_test_data_mcd_file: MCDFile):
parser = MCDParser(imc_test_data_mcd_file.schema_xml)
slides = parser.parse_slides()
assert len(slides) == 1
slide = slides[0]
assert slide.id == 0
assert slide.description == "Slide"
assert slide.width_um == 75000.0
assert slide.height_um == 25000.0
assert len(slide.panoramas) == 1
assert len(slide.acquisitions) == 3
panorama = next(p for p in slide.panoramas if p.id == 1)
assert panorama.slide == slide
assert panorama.id == 1
assert panorama.description == "Panorama_001"
assert panorama.width_um == 193.0
assert panorama.height_um == 162.0
assert panorama.points_um == (
(31020.0, 13486.0),
(31213.0, 13486.0),
(31213.0, 13324.0),
(31020.0, 13324.0),
)
assert len(panorama.acquisitions) == 0
acquisition = next(a for a in slide.acquisitions if a.id == 1)
assert acquisition.slide == slide
assert acquisition.panorama is None
assert acquisition.id == 1
assert acquisition.description == "ROI_001"
assert acquisition.width_px == 60
assert acquisition.height_px == 60
assert acquisition.pixel_size_x_um == 1.0
assert acquisition.pixel_size_y_um == 1.0
assert acquisition.width_um == 60.0
assert acquisition.height_um == 60.0
assert acquisition.num_channels == 5
assert tuple(acquisition.channel_metals) == (
"Ag",
"Pr",
"Sm",
"Eu",
"Yb",
)
assert tuple(acquisition.channel_masses) == (107, 141, 147, 153, 172)
assert tuple(acquisition.channel_labels) == (
"107Ag",
"Cytoker_651((3356))Pr141",
"Laminin_681((851))Sm147",
"YBX1_2987((3532))Eu153",
"H3K27Ac_1977((2242))Yb172",
)
assert tuple(acquisition.channel_names) == (
"Ag107",
"Pr141",
"Sm147",
"Eu153",
"Yb172",
)
assert acquisition.roi_points_um == (
(31080.0, 13449.0),
(31140.0, 13449.0),
(31140.0, 13389.0),
(31080.0, 13389.0),
)
assert acquisition.roi_coords_um == (
(31080.0, 13449.0),
(31139.799043811327, 13450.084762417044),
(31140.501, 13390.28),
(31080.701956188677, 13389.195237582955),
)
@pytest.mark.skipif(not damond_mcd_file_path.exists(), reason="data not available")
def test_schema_xml_damond(self):
pass # TODO
@pytest.mark.skipif(not damond_mcd_file_path.exists(), reason="data not available")
def test_schema_xml_elem_damond(self):
pass # TODO
@pytest.mark.skipif(not damond_mcd_file_path.exists(), reason="data not available")
def test_schema_xml_xmlns_damond(self):
pass # TODO
@pytest.mark.skipif(not damond_mcd_file_path.exists(), reason="data not available")
def test_parse_slides_damond(self):
parser = MCDParser(self.damond_mcd_file.schema_xml)
slides = parser.parse_slides()
assert len(slides) == 1
slide = slides[0]
assert slide.id == 1
assert slide.description == "compensationslide1000"
assert slide.width_um == 75000.0
assert slide.height_um == 25000.0
assert len(slide.panoramas) == 8
assert len(slide.acquisitions) == 41
panorama = next(p for p in slide.panoramas if p.id == 1)
assert panorama.slide == slide
assert panorama.id == 1
assert panorama.description == "TuningTape"
assert panorama.width_um == 1472.9184890671672
assert panorama.height_um == 1526.6011674842225
assert panorama.points_um == (
(28961.0, 6460.0),
(30433.682653484964, 6486.356736527695),
(30461.0, 4960.0),
(28988.317346515036, 4933.643263472244),
)
assert len(panorama.acquisitions) == 5
acquisition = next(a for a in panorama.acquisitions if a.id == 1)
assert acquisition.slide == slide
assert acquisition.panorama == panorama
assert acquisition.id == 1
assert acquisition.description == "TT_G01"
assert acquisition.width_px == 51
assert acquisition.height_px == 50
assert acquisition.pixel_size_x_um == 1.0
assert acquisition.pixel_size_y_um == 1.0
assert acquisition.width_um == 51.0
assert acquisition.height_um == 50.0
assert acquisition.num_channels == 3
assert tuple(acquisition.channel_metals) == ("Eu", "Eu", "Lu")
assert tuple(acquisition.channel_masses) == (151, 153, 175)
assert tuple(acquisition.channel_labels) == ("151Eu", "153Eu", "175Lu")
assert tuple(acquisition.channel_names) == ("Eu151", "Eu153", "Lu175")
assert acquisition.roi_points_um == (
(29195.563447789347, 6091.267354770278),
(29245.675268795687, 6091.269356041085),
(29245.67326752488, 6041.381177047424),
(29195.781085989598, 6041.606820330908),
)
assert acquisition.roi_coords_um is None