Disabled synthetic tests by default, added some analysis

Author: etpeterson

pytest.ini

@@ -0,0 +1,5 @@
+[pytest]
+markers =
+    slow: marks tests as slow (deselect with '-m "not slow"')
+addopts =  
+    -m 'not slow'

tests/IVIMmodels/unit_tests/analyze.r

@@ -0,0 +1,21 @@
+library(tidyverse)
+data <- read.csv("test_output.csv", skip=1, col.names=c("Algorithm", "Region", "SNR", "Truth", "Fitted"))
+data<-separate_wider_delim(data, cols = Truth, delim = ",", names = c("f", "D", "Dp"))
+data$f <- substring(data$f, 2)
+data$Dp <- substring(data$Dp, 1, nchar(data$Dp) - 1)
+data<-separate_wider_delim(data, cols = Fitted, delim = ",", names = c("f_fitted", "D_fitted", "Dp_fitted"))
+data$f_fitted <- substring(data$f_fitted, 2)
+data$Dp_fitted <- substring(data$Dp_fitted, 1, nchar(data$Dp_fitted) - 1)
+data[c("Algorithm", "Region")] <- sapply(data[c("Algorithm", "Region")], as.factor)
+data[c("SNR", "f", "D", "Dp", "f_fitted", "D_fitted", "Dp_fitted")] <- sapply(data[c("SNR", "f", "D", "Dp", "f_fitted", "D_fitted", "Dp_fitted")], as.numeric)
+ggplot(data, aes(x=Algorithm)) + geom_boxplot(aes(y=f_fitted)) + geom_boxplot(color="red", aes(y=f)) + facet_grid(SNR ~ Region) + scale_x_discrete(guide = guide_axis(angle = 90)) + ylim(0, 1) + ggtitle("Perfusion fraction grid") + xlab("Perfusion fraction")
+ggsave("f.pdf", width = 50, height = 50, units = "cm")
+ggplot(data, aes(x=Algorithm)) + geom_boxplot(aes(y=D_fitted)) + geom_boxplot(color="red", aes(y=D)) + facet_grid(SNR ~ Region) + scale_x_discrete(guide = guide_axis(angle = 90)) + ggtitle("Diffusion grid") + xlab("Diffusion")
+ggsave("D.pdf", width = 50, height = 50, units = "cm")
+ggplot(data, aes(x=Algorithm)) + geom_boxplot(aes(y=Dp_fitted)) + geom_boxplot(color="red", aes(y=Dp)) + facet_grid(SNR ~ Region) + scale_x_discrete(guide = guide_axis(angle = 90)) + ggtitle("Perfusion grid") + xlab("Perfusion")
+ggsave("Dp.pdf", width = 50, height = 50, units = "cm")
+#why?
+ggplot(data, aes(x=Algorithm)) + geom_boxplot(aes(y=D_fitted)) + geom_boxplot(color="red", aes(y=Dp)) + facet_grid(SNR ~ Region) + scale_x_discrete(guide = guide_axis(angle = 90)) + ggtitle("Diffusion grid") + xlab("Diffusion")
+ggsave("D_tweak.pdf", width = 50, height = 50, units = "cm")
+ggplot(data, aes(x=Algorithm)) + geom_boxplot(aes(y=Dp_fitted)) + geom_boxplot(color="red", aes(y=D)) + facet_grid(SNR ~ Region) + scale_x_discrete(guide = guide_axis(angle = 90)) + ggtitle("Perfusion grid") + xlab("Perfusion")
+ggsave("Dp_tweak.pdf", width = 50, height = 50, units = "cm")

tests/IVIMmodels/unit_tests/test_ivim_synthetic.py

@@ -11,7 +11,8 @@
 from utilities.data_simulation.GenerateData import GenerateData
 
 #run using pytest <path_to_this_file> --saveFileName test_output.txt --SNR 50 100 200
-#e.g. pytest tests/IVIMmodels/unit_tests/test_ivim_synthetic.py --saveFileName test_output.txt --SNR 50 100 200
+#e.g. pytest -m slow tests/IVIMmodels/unit_tests/test_ivim_synthetic.py  --saveFileName test_output.csv --SNR 10 50 100 200 --fitCount 20
+@pytest.mark.slow
 def test_generated(ivim_algorithm, ivim_data, SNR, rtol, atol, fit_count, save_file):
     # assert save_file == "test"
     random.seed(42)