def test_create_feature_map(self):
test_set = {"001": (2100, 3800, 2400, 4000),
"003": (2400, 4700, 2600, 4850)}
id = "003"
roi = test_set[id]
x1 = roi[0]
y1 = roi[1]
x2 = roi[2]
y2 = roi[3]
c = Params()
c.load_config_file(JSON_PATH)
imgCone = ImageCone(c, Open_Slide())
# 读取数字全扫描切片图像
tag = imgCone.open_slide("Tumor/Tumor_%s.tif" % id,
'Tumor/tumor_%s.xml' % id, "Tumor_%s" % id)
# encoder = EncoderFactory(self._params, "idec", "AE_500_32", 16)
encoder = EncoderFactory(c, "cae", "AE_500_32", 16)
seg = Segmentation(c, imgCone, encoder)
# global_seeds = seg.get_seeds_for_seg(x1, y1, x2, y2, 1.25)
# print(global_seeds)
f_map = seg.create_feature_map(x1, y1, x2, y2, 1.25, 5)
print(f_map.shape)
np.save("feature_map", f_map)
def test_create_superpixels(self):
test_set = [("001", 2100, 3800, 2400, 4000),
("003", 2400, 4700, 2600, 4850)]
id = 1
roi = test_set[id]
slice_id = roi[0]
x1 = roi[1]
y1 = roi[2]
x2 = roi[3]
y2 = roi[4]
c = Params()
c.load_config_file(JSON_PATH)
imgCone = ImageCone(c, Open_Slide())
# 读取数字全扫描切片图像
tag = imgCone.open_slide("Tumor/Tumor_%s.tif" % slice_id,
'Tumor/tumor_%s.xml' % slice_id, "Tumor_%s" % slice_id)
seg = Segmentation(c, imgCone)
f_map = seg.create_feature_map(x1, y1, x2, y2, 1.25, 5)
label_map = seg.create_superpixels(f_map, 0.4, iter_num = 3)
print(label_map.shape)
np.save("label_map", label_map)
def test_extract_feature(self):
c = Params()
c.load_config_file(JSON_PATH)
model_name = "cae"
sample_name = "cifar10"
ae = EncoderFactory(c, model_name, sample_name)
ae.extract_feature(None)
def test_train_model5(self):
c = Params()
c.load_config_file(JSON_PATH)
model_name = "aae"
sample_name = "AE_500_32"
ae = EncoderFactory(c, model_name, sample_name, z_dim=64)
ae.train_adversarial_ae(batch_size=64, epochs=50)
def test_train_model3(self):
c = Params()
c.load_config_file(JSON_PATH)
model_name = "ccae"
sample_name = "cifar10"
ae = EncoderFactory(c, model_name, sample_name)
ae.train_ae(batch_size=64, epochs=50)
def test_train_idec(self):
c = Params()
c.load_config_file(JSON_PATH)
model_name = "idec"
sample_name = "AE_500_32"
idec = EncoderFactory(c, model_name, sample_name, 64)
idec.train_idec(batch_size=64, epochs=100)
def test_pack_samples_DSC_256(self):
c = Params()
c.load_config_file(JSON_PATH)
pack = PatchPack(c)
pack.create_train_test_data_DSC("P0619", [
"S2000_256_cancer", "S2000_256_normal", "S2000_256_normal2",
"S2000_256_edgeinner", "S2000_256_edgeouter"
], "T2_P0619_4000_256", 40, 20)
def test_calc_patch_cancer_ratio(self):
c = Params()
c.load_config_file(JSON_PATH)
pack = PatchPack(c)
pack.calc_patch_cancer_ratio("P0619", [
"S2000_256_edgeinner", "S2000_256_edgeouter", "S2000_256_cancer",
"S2000_256_normal", "S4000_256_edgeinner", "S4000_256_edgeouter",
"S4000_256_cancer", "S4000_256_normal"
])
def test_eval_latent_weight(self):
c = Params()
c.load_config_file(JSON_PATH)
model_name = "cae"
sample_name = "AE_500_32"
ae = EncoderFactory(c, model_name, sample_name, 64)
result = ae.eval_latent_vector_loss(batch_size=64)
np.save("latent_vector_loss_{}".format(model_name), result)
def test_no_plot_msg(params: Params) -> None:
params.color_space = RGB # type: ignore
params.plot = True # type: ignore
captured_output = io.StringIO()
sys.stdout = captured_output
app.run(FDM, params)
sys.stdout = sys.__stdout__
expected = 'Plotting is not implemented for operation fdm!\n'
assert captured_output.getvalue() == expected
os.remove(params.result_path)
def test_calc_latent_vector_weight(self):
c = Params()
c.load_config_file(JSON_PATH)
model_name = "cae"
sample_name = "AE_500_32"
ae = EncoderFactory(c, model_name, sample_name, 16)
loss = np.load("latent_vector_loss_{}.npy".format(model_name))
print(loss)
def test_02(self):
c = Params()
c.load_config_file(JSON_PATH)
model_name = "cae"
sample_name = "AE_500_32"
ae = EncoderFactory(c, model_name, sample_name, 16)
model = ae.create_initial_model()
from torchsummary import summary
summary(model, input_size=(3, 32, 32), device="cpu")
def test_read_patch_db(self):
c = Params()
c.load_config_file(JSON_PATH)
patches_code = "P0619"
root_path = c.PATCHS_ROOT_PATH[patches_code]
data = np.load('{}/patch_mask_ratio.npy'.format(root_path),
allow_pickle=True)
patch_db = data[()]
print(len(patch_db.values()))
plt.hist(patch_db.values(), bins=20, range=(0., 1), log=True)
plt.show()
def test_pack_samples_MSC(self):
c = Params()
c.load_config_file(JSON_PATH)
pack = PatchPack(c)
pack.create_train_test_data_MSC({
10: "S1000",
20: "S2000",
40: "S4000"
}, {
"256_cancer": (1, 3),
"256_edgeinner": (1, 2),
"256_edgeouter": (0, 1),
"256_normal": (0, 0),
}, 0, 1, "T_NC2_msc_256")
def test_params_len() -> None:
mapping_1 = {'a': 1, 'b': 2, 'c': 3}
mapping_2 = {'a': 1, 'b': 2, 'c': 3}
params_1 = Params(mapping_1)
params_2 = Params(mapping_2)
assert len(params_1) == len(params_2)
assert len(params_1) == len(mapping_1)
assert len(params_2) == len(mapping_2)
mapping_2 = {'a': 1, 'b': 2, 'c': 3, 'd': 4}
params_2 = Params(mapping_2)
assert len(params_1) != len(params_2)
assert len(params_2) == len(mapping_2)
def test_make_plot(color_space: str, image_channels: str, source_path: str,
reference_path: str) -> None:
params = Params(
{
'color_space': color_space,
'channels': image_channels,
'match_proportion': 0.8,
'src_path': source_path,
'ref_path': reference_path
}
)
converter = build_cs_converter(params.color_space)
source = read_image(params.src_path)
reference = read_image(params.ref_path)
source = converter.convert(source)
reference = converter.convert(reference)
channels = tuple(int(c) for c in params.channels.split(','))
hist_match = HistogramMatching(channels, params.match_proportion)
result = hist_match(source, reference)
file_name = os.path.join(TEST_DIR, 'histogram_matching_plot.png')
images = hm_plot.Images(source, reference, result)
hm_plot.make_plot(file_name, images, converter, params.color_space,
params.channels)
assert os.path.exists(file_name) is True
os.remove(file_name)
def test_params_str() -> None:
mapping = {'a': 10, 'b': 'abc'}
params = Params(mapping)
# dict is a hash table, so there is no order guarantee
params_str_1 = 'a : 10\nb : abc\n'
params_str_2 = 'b : abc\na : 10\n'
assert str(params) == params_str_1 or str(params) == params_str_2
def test_extract_feature(self):
c = Params()
c.load_config_file(JSON_PATH)
model_name = "densenet121"
imgCone = ImageCone(c, Open_Slide())
# 读取数字全扫描切片图像
tag = imgCone.open_slide("Tumor/Tumor_004.tif",
None, "Tumor_004")
seeds = [(34816, 48960), (35200, 48640), (12800, 56832)] # C, C, S,
fe = Transfer(c, model_name, None)
# result = fe.extract_feature(imgCone, 20, 256, seeds, 2)
result = fe.svm_predict_on_batch(imgCone, 20, 256, seeds, 2)
print(result)
def test_pack_samples_2000_256(self):
c = Params()
c.load_config_file(JSON_PATH)
pack = PatchPack(c)
data_tag = pack.initialize_sample_tags_byMask("P0619", [
"S2000_256_cancer", "S2000_256_normal", "S2000_256_normal2",
"S2000_256_edgeinner", "S2000_256_edgeouter"
])
# data_tag = pack.filtering(data_tag, filter_mask=["Tumor_033", "Tumor_034",
# "Tumor_046","Tumor_054","Tumor_061"])
pack.create_train_test_data(data_tag,
0.95,
0.05,
"S1_P0619_2000_256",
need_balance=True)
def test_train_top_svm(self):
MODEL_NAME = "densenet121"
# SAMPLE_FIlENAME = "T_NC_500_128"
# SAMPLE_FIlENAME = "T_NC_2000_256"
SAMPLE_FIlENAME = "T_NC_4000_256"
PATCH_TYPE = "4000_256"
# PATCH_TYPE = "2000_256"
# PATCH_TYPE = "500_128"
train_file = "{}_{}_train_features.npz".format(MODEL_NAME, SAMPLE_FIlENAME)
test_file = "{}_{}_test_features.npz".format(MODEL_NAME, SAMPLE_FIlENAME)
c = Params()
c.load_config_file(JSON_PATH)
cnn = Transfer(c, MODEL_NAME, PATCH_TYPE)
cnn.train_top_svm(train_file, test_file)
def test_params_dict(data_member_name: str) -> None:
mapping_1 = {'a': 1, 'b': 2, 'c': 3}
mapping_2 = {'a': 1, 'b': 2, 'c': 3}
params_1 = Params(mapping_1)
params_2 = Params(mapping_2)
assert len(params_1.__dict__[data_member_name]) == \
len(params_2.__dict__[data_member_name])
assert params_1.__dict__[data_member_name] == \
params_2.__dict__[data_member_name]
mapping_2 = {'a': 1, 'b': 2, 'c': 3, 'd': 4}
params_2 = Params(mapping_2)
assert len(params_1.__dict__[data_member_name]) != \
len(params_2.__dict__[data_member_name])
assert params_1.__dict__[data_member_name] != \
params_2.__dict__[data_member_name]
def fixture_params() -> Params:
return Params({
'color_space': GRAY,
'channels': '0,1,2',
'match_proportion': MATCH_FULL,
'verify_input': True,
'plot': False,
'source_path': MUNICH_1_PATH,
'reference_path': MUNICH_2_PATH,
'result_path': 'application_run_test.png'
})
def test_show_sample_txt(self):
c = Params()
c.load_config_file(
"D:/CloudSpace/WorkSpace/PatholImage/config/justin2.json")
sample_txt = "{}/{}".format(c.PATCHS_ROOT_PATH,
"S500_128_False_normal.txt")
patch_path = c.PATCHS_ROOT_PATH
filenames_list, labels_list = read_csv_file(patch_path, sample_txt)
fig = plt.figure(figsize=(8, 10), dpi=100)
for index, filename in enumerate(filenames_list):
img = imread(filename)
pos = index % 20
plt.subplot(4, 5, pos + 1)
plt.imshow(img)
plt.axis("off")
if pos == 19:
fig.tight_layout() # 调整整体空白
plt.subplots_adjust(wspace=0, hspace=0) # 调整子图间距
plt.show()
def test_compare_save_file(self):
c = Params()
c.load_config_file(JSON_PATH)
import numpy as np
filename = "densenet121_T_NC_2000_256_test_features.npz"
data_path = "{}/data/pytorch/{}".format(c.PROJECT_ROOT, filename)
D = np.load(data_path)
test_features = D['arr_0']
test_label = D['arr_1']
data_path = "{}/data/keras/{}".format(c.PROJECT_ROOT, filename)
D = np.load(data_path)
test_features2 = D['arr_0']
test_label2 = D['arr_1']
d = (test_features - test_features2)
mean = np.mean(d)
std = np.std(d)
print(mean, std)
mean = np.mean(test_features)
std = np.std(test_features)
print(mean, std)
def test_operation_context_builder() -> None:
params = Params({'color_space': RGB,
'channels': '0,1,2',
'match_proportion': 1.0,
'verify_input': True})
op_ctx = operation_context_builder.build_operation_context(HM, params)
assert isinstance(op_ctx.operation, HistogramMatching)
assert isinstance(op_ctx.converter, ColorSpaceConverter)
op_ctx = operation_context_builder.build_operation_context(FDM, params)
assert isinstance(op_ctx.operation, FeatureDistributionMatching)
assert isinstance(op_ctx.converter, ColorSpaceConverter)
with pytest.raises(ValueError):
operation_context_builder.build_operation_context('1337', params)
def fixture_params() -> Params:
mapping = {'param_1': 10, 'param_2': 'abc', 'param_3': 2.45}
return Params(mapping)
def run(ctx: click.core.Context) -> None:
""" Calls the main program with the parameters available in the context """
application.run(ctx.command.name, Params(ctx.obj))
def test_params_python_keyword() -> None:
mapping = {'a': 1, 'b': 2, 'import': 3}
with pytest.raises(NameError):
assert Params(mapping)
def test_params_wrong_identifier() -> None:
mapping = {'a': 1, 'b': 2, '3.14x': 3}
with pytest.raises(NameError):
assert Params(mapping)
def test_params_wrong_name_type() -> None:
mapping = {'a': 1, 'b': 2, 3: 'xyz'}
with pytest.raises(TypeError):
assert Params(mapping) # type: ignore