def test_wsireg_run_reg_reload_from_cache(data_out_dir, im_mch_np):
img_fp1 = im_mch_np
output_dir = str(data_out_dir)
pname = gen_project_name_str()
wsi_reg = WsiReg2D(pname, output_dir)
wsi_reg.add_modality(
"mod1",
img_fp1,
0.65,
channel_names=["test"],
channel_colors=["red"],
)
wsi_reg.add_modality(
"mod2",
img_fp1,
0.65,
channel_names=["test"],
channel_colors=["red"],
)
wsi_reg.add_reg_path("mod1", "mod2", reg_params=["rigid_test"])
wsi_reg.register_images()
pp_mod1_r1 = imread(wsi_reg.image_cache / "mod1_prepro.tiff")
pp_mod2_r1 = imread(wsi_reg.image_cache / "mod2_prepro.tiff")
# run registration again, loading data from cache
wsi_reg = WsiReg2D(pname, output_dir)
wsi_reg.add_modality(
"mod1",
img_fp1,
0.65,
channel_names=["test"],
channel_colors=["red"],
preprocessing={"ch_indices": [1]},
)
wsi_reg.add_modality(
"mod2",
img_fp1,
0.65,
channel_names=["test"],
channel_colors=["red"],
preprocessing={"ch_indices": [1]},
)
wsi_reg.add_reg_path("mod1", "mod2", reg_params=["rigid_test"])
wsi_reg.register_images()
pp_mod1_r2 = imread(wsi_reg.image_cache / "mod1_prepro.tiff")
pp_mod2_r2 = imread(wsi_reg.image_cache / "mod2_prepro.tiff")
assert not np.array_equal(pp_mod1_r1, pp_mod1_r2)
assert not np.array_equal(pp_mod2_r1, pp_mod2_r2)
def test_wsireg_run_reg_downsampling_m1m2_merge_no_prepro(
data_out_dir, disk_im_gry):
wsi_reg = WsiReg2D(gen_project_name_str(), str(data_out_dir))
img_fp1 = str(disk_im_gry)
wsi_reg.add_modality(
"mod1",
img_fp1,
0.65,
channel_names=["test"],
channel_colors=["red"],
preprocessing={"downsampling": 2},
)
wsi_reg.add_modality(
"mod2",
img_fp1,
0.65,
channel_names=["test"],
channel_colors=["red"],
preprocessing={"downsampling": 2},
)
wsi_reg.add_reg_path("mod1", "mod2", reg_params=["rigid_test"])
wsi_reg.add_merge_modalities("mod12-merge", ["mod1", "mod2"])
wsi_reg.register_images()
im_fps = wsi_reg.transform_images(transform_non_reg=False,
remove_merged=True)
regim = reg_image_loader(im_fps[0], 0.65)
assert regim.shape == (2, 2048, 2048)
def test_wsireg_run_reg_downsampling_m1m2_changeores(data_out_dir,
disk_im_gry):
wsi_reg = WsiReg2D(gen_project_name_str(), str(data_out_dir))
img_fp1 = str(disk_im_gry)
wsi_reg.add_modality(
"mod1",
img_fp1,
0.65,
channel_names=["test"],
channel_colors=["red"],
preprocessing={"downsampling": 2},
output_res=(1.3, 1.3),
)
wsi_reg.add_modality(
"mod2",
img_fp1,
0.65,
channel_names=["test"],
channel_colors=["red"],
preprocessing={"downsampling": 2},
)
wsi_reg.add_reg_path("mod1", "mod2", reg_params=["rigid_test"])
wsi_reg.register_images()
im_fps = wsi_reg.transform_images(transform_non_reg=False)
regim = reg_image_loader(im_fps[0], 0.65)
assert regim.shape[1:] == (1024, 1024)
def test_wsireg_run_reg_changeres(data_out_dir, disk_im_gry):
wsi_reg = WsiReg2D(gen_project_name_str(), str(data_out_dir))
img_fp1 = str(disk_im_gry)
wsi_reg.add_modality(
"mod1",
img_fp1,
0.65,
channel_names=["test"],
channel_colors=["red"],
output_res=0.325,
)
wsi_reg.add_modality(
"mod2",
img_fp1,
0.65,
channel_names=["test"],
channel_colors=["red"],
)
wsi_reg.add_reg_path("mod1",
"mod2",
reg_params=["rigid_test", "affine_test"])
wsi_reg.register_images()
im_fps = wsi_reg.transform_images(transform_non_reg=False)
regim = reg_image_loader(im_fps[0], 0.325)
assert regim.shape[1:] == (4096, 4096)
def test_wsireg_run_reg_shapes(data_out_dir, disk_im_gry):
wsi_reg = WsiReg2D(gen_project_name_str(), str(data_out_dir))
img_fp1 = str(disk_im_gry)
wsi_reg.add_modality(
"mod1",
img_fp1,
0.65,
channel_names=["test"],
channel_colors=["red"],
)
wsi_reg.add_modality(
"mod2",
img_fp1,
0.65,
channel_names=["test"],
channel_colors=["red"],
)
wsi_reg.add_reg_path("mod1",
"mod2",
reg_params=["rigid_test", "affine_test"])
wsi_reg.add_attachment_shapes("mod1", "shapeset", GEOJSON_FP)
wsi_reg.register_images()
wsi_reg.transform_shapes()
wsi_reg.save_transformations()
im_fps = wsi_reg.transform_images(transform_non_reg=False)
gj_files = sorted(Path(im_fps[0]).parent.glob("*.geojson"))
assert Path(im_fps[0]).exists() is True
assert len(gj_files) > 0
def test_wsireg_run_reg_wmerge(data_out_dir, disk_im_gry):
wsi_reg = WsiReg2D(gen_project_name_str(), str(data_out_dir))
img_fp1 = str(disk_im_gry)
wsi_reg.add_modality(
"mod1",
img_fp1,
0.65,
channel_names=["test"],
channel_colors=["red"],
)
wsi_reg.add_modality(
"mod2",
img_fp1,
0.65,
channel_names=["test"],
channel_colors=["red"],
)
wsi_reg.add_reg_path("mod1",
"mod2",
reg_params=["rigid_test", "affine_test"])
wsi_reg.add_merge_modalities("test_merge", ["mod1", "mod2"])
wsi_reg.register_images()
wsi_reg.save_transformations()
im_fps = wsi_reg.transform_images(transform_non_reg=True)
merged_im = reg_image_loader(im_fps[0], 0.65)
assert Path(im_fps[0]).exists() is True
assert merged_im.shape == (2, 2048, 2048)
def test_wsireg_run_reg_w_override(data_out_dir, im_mch_np):
wsi_reg = WsiReg2D(gen_project_name_str(), str(data_out_dir))
img_fp1 = im_mch_np
wsi_reg.add_modality(
"mod1",
img_fp1,
0.65,
channel_names=["test"],
channel_colors=["red"],
)
wsi_reg.add_modality(
"mod2",
img_fp1,
0.65,
channel_names=["test"],
channel_colors=["red"],
)
wsi_reg.add_modality(
"mod3",
img_fp1,
0.65,
channel_names=["test"],
channel_colors=["red"],
)
wsi_reg.add_modality(
"mod4",
img_fp1,
0.65,
channel_names=["test"],
channel_colors=["red"],
)
wsi_reg.add_reg_path("mod1", "mod2", reg_params=["rigid_test"])
wsi_reg.add_reg_path("mod4", "mod3", reg_params=["rigid_test"])
wsi_reg.add_reg_path(
"mod2",
"mod3",
reg_params=["rigid_test"],
override_prepro={
"source": {
"ch_indices": [1]
},
"target": {
"ch_indices": [1]
},
},
)
wsi_reg.register_images()
or_mod2 = imread(wsi_reg.image_cache / "mod2-mod3-override_prepro.tiff")
or_mod3 = imread(wsi_reg.image_cache / "mod3-mod2-override_prepro.tiff")
pp_mod2 = imread(wsi_reg.image_cache / "mod2_prepro.tiff")
pp_mod3 = imread(wsi_reg.image_cache / "mod3_prepro.tiff")
assert not np.array_equal(or_mod2, pp_mod2)
assert not np.array_equal(or_mod3, pp_mod3)
def config_to_WsiReg2D(config_filepath, output_dir):
reg_config = parse_check_reg_config(config_filepath)
reg_graph = WsiReg2D(
reg_config.get("project_name"),
output_dir,
reg_config.get("cache_images"),
)
return reg_graph
def test_wsireg_run_reg_with_crop_merge(data_out_dir, disk_im_gry):
wsi_reg = WsiReg2D(gen_project_name_str(), str(data_out_dir))
img_fp1 = str(disk_im_gry)
wsi_reg.add_modality(
"mod1",
img_fp1,
0.65,
channel_names=["test"],
channel_colors=["red"],
)
wsi_reg.add_modality(
"mod2",
img_fp1,
0.65,
channel_names=["test"],
channel_colors=["red"],
)
wsi_reg.add_modality(
"mod3",
img_fp1,
0.65,
channel_names=["test"],
channel_colors=["red"],
preprocessing={
"mask_bbox": [512, 512, 512, 512],
"crop_to_mask_bbox": True,
},
)
wsi_reg.add_reg_path("mod1", "mod3", reg_params=["rigid_test"])
wsi_reg.add_reg_path("mod2", "mod3", reg_params=["rigid_test"])
wsi_reg.register_images()
wsi_reg.add_merge_modalities("merge", ["mod1", "mod2", "mod3"])
# not cropped
im_fps = wsi_reg.transform_images(transform_non_reg=True,
to_original_size=True)
registered_image_nocrop = reg_image_loader(im_fps[0], 1)
# crop image
im_fps = wsi_reg.transform_images(transform_non_reg=True,
to_original_size=False)
wsi_reg.save_transformations()
registered_image_crop = reg_image_loader(im_fps[0], 1)
assert registered_image_nocrop.shape[1:] == (2048, 2048)
assert registered_image_crop.shape[1:] == (512, 512)
def test_wsireg_run_reg_downsampling_m1m2_merge_ds_attach(
data_out_dir, disk_im_gry):
wsi_reg = WsiReg2D(gen_project_name_str(), str(data_out_dir))
img_fp1 = str(disk_im_gry)
wsi_reg.add_modality(
"mod1",
img_fp1,
0.65,
channel_names=["test"],
channel_colors=["red"],
preprocessing={"downsampling": 2},
)
wsi_reg.add_modality(
"mod2",
img_fp1,
0.65,
channel_names=["test"],
channel_colors=["red"],
preprocessing={"downsampling": 2},
)
wsi_reg.add_attachment_images(
"mod2",
"mod3",
img_fp1,
0.65,
channel_names=["test"],
channel_colors=["red"],
)
wsi_reg.add_reg_path("mod1", "mod2", reg_params=["rigid_test"])
wsi_reg.add_merge_modalities("mod12-merge", ["mod1", "mod2", "mod3"])
wsi_reg.register_images()
im_fps = wsi_reg.transform_images(transform_non_reg=False,
remove_merged=True)
regim = reg_image_loader(im_fps[0], 0.65)
ome_data = from_xml(TiffFile(im_fps[0]).ome_metadata)
assert regim.shape == (3, 2048, 2048)
assert ome_data.images[0].pixels.physical_size_x == 0.65
assert ome_data.images[0].pixels.physical_size_y == 0.65
assert ome_data.images[0].pixels.size_x == 2048
assert ome_data.images[0].pixels.size_y == 2048
assert ome_data.images[0].pixels.size_c == 3
def test_wsireg_run_reg_wattachment_ds2(data_out_dir, disk_im_gry):
wsi_reg = WsiReg2D(gen_project_name_str(), str(data_out_dir))
im1 = np.random.randint(0, 255, (2048, 2048), dtype=np.uint16)
im2 = np.random.randint(0, 255, (2048, 2048), dtype=np.uint16)
wsi_reg.add_modality(
"mod1",
im1,
0.65,
channel_names=["test"],
channel_colors=["red"],
preprocessing={"downsampling": 2},
)
wsi_reg.add_modality(
"mod2",
im2,
0.65,
channel_names=["test"],
channel_colors=["red"],
preprocessing={"downsampling": 2},
)
wsi_reg.add_attachment_images("mod2", "attached", im2, image_res=0.65)
wsi_reg.add_attachment_images("mod1", "attached2", im1, image_res=0.65)
wsi_reg.add_reg_path("mod2",
"mod1",
reg_params=["rigid_test", "affine_test"])
wsi_reg.register_images()
im_fps = wsi_reg.transform_images(transform_non_reg=False)
wsi_reg.save_transformations()
regim = reg_image_loader(im_fps[0], 0.65)
attachim = reg_image_loader(im_fps[1], 0.65)
attachim2 = reg_image_loader(im_fps[2], 0.65)
assert np.array_equal(
np.squeeze(regim.dask_image.compute()),
np.squeeze(attachim.dask_image.compute()),
)
assert np.array_equal(np.squeeze(im1),
np.squeeze(attachim2.dask_image.compute()))
def test_wsireg2d_add_merge_modality_notfound(data_out_dir, data_im_fp):
wsi_reg = WsiReg2D(gen_project_name_str(), str(data_out_dir))
img_fp1 = str(data_im_fp)
wsi_reg.add_modality(
"test_mod1",
img_fp1,
0.65,
channel_names=["test"],
channel_colors=["red"],
)
img_fp1 = str(data_im_fp)
wsi_reg.add_modality(
"test_mod2",
img_fp1,
0.65,
channel_names=["test"],
channel_colors=["red"],
)
with pytest.raises(ValueError):
wsi_reg.add_merge_modalities("mergetest", ["test_mod1", "test_mod3"])
def test_wsireg_run_reg_downsampling_from_cache(data_out_dir, disk_im_gry):
pstr = gen_project_name_str()
wsi_reg = WsiReg2D(pstr, str(data_out_dir))
img_fp1 = str(disk_im_gry)
wsi_reg.add_modality(
"mod1",
img_fp1,
0.65,
channel_names=["test"],
channel_colors=["red"],
preprocessing={"downsampling": 2},
)
wsi_reg.add_modality(
"mod2",
img_fp1,
0.65,
channel_names=["test"],
channel_colors=["red"],
preprocessing={"downsampling": 2},
)
wsi_reg.add_attachment_images(
"mod2",
"mod3",
img_fp1,
0.65,
channel_names=["test"],
channel_colors=["red"],
)
wsi_reg.add_reg_path("mod1", "mod2", reg_params=["rigid_test"])
wsi_reg.register_images()
im_fps_nocache = wsi_reg.transform_images(transform_non_reg=True,
remove_merged=True)
regim_nocache = reg_image_loader(im_fps_nocache[0], 0.65)
regim_nocache_attach = reg_image_loader(im_fps_nocache[1], 0.65)
regim_nocache_br = reg_image_loader(im_fps_nocache[2], 0.65)
wsi_reg2 = WsiReg2D(pstr, str(data_out_dir))
img_fp1 = str(disk_im_gry)
wsi_reg2.add_modality(
"mod1",
img_fp1,
0.65,
channel_names=["test"],
channel_colors=["red"],
preprocessing={"downsampling": 2},
)
wsi_reg2.add_modality(
"mod2",
img_fp1,
0.65,
channel_names=["test"],
channel_colors=["red"],
preprocessing={"downsampling": 2},
)
wsi_reg2.add_attachment_images(
"mod2",
"mod3",
img_fp1,
0.65,
channel_names=["test"],
channel_colors=["red"],
)
wsi_reg2.add_reg_path("mod1", "mod2", reg_params=["rigid_test"])
wsi_reg2.register_images()
im_fps_cache = wsi_reg.transform_images(transform_non_reg=True,
remove_merged=True)
regim_cache = reg_image_loader(im_fps_cache[0], 0.65)
regim_cache_attach = reg_image_loader(im_fps_cache[1], 0.65)
regim_cache_br = reg_image_loader(im_fps_cache[2], 0.65)
assert regim_cache.shape == regim_nocache.shape
assert regim_cache_br.shape == regim_nocache_br.shape
assert regim_cache_attach.shape == regim_nocache_attach.shape
def test_WsiReg2D_instantiation(data_out_dir):
pstr = gen_project_name_str()
wsi_reg = WsiReg2D(pstr, str(data_out_dir))
assert wsi_reg.project_name == pstr
assert wsi_reg.output_dir == Path(str(data_out_dir))