From 835ea8c1d8eaf7731f48c1eb8a4f7cf87e5ef34b Mon Sep 17 00:00:00 2001
From: Michiel Cottaar <MichielCottaar@protonmail.com>
Date: Wed, 11 Dec 2019 13:52:42 +0000
Subject: [PATCH] DOC: update documentation
---
unit_tests/fdt/dtifit/feedsRun | 28 +++++++++++++++++++++++++---
1 file changed, 25 insertions(+), 3 deletions(-)
diff --git a/unit_tests/fdt/dtifit/feedsRun b/unit_tests/fdt/dtifit/feedsRun
index f923690..d6ddd43 100755
--- a/unit_tests/fdt/dtifit/feedsRun
+++ b/unit_tests/fdt/dtifit/feedsRun
@@ -1,6 +1,8 @@
#!/usr/bin/env fslpython
"""
-Generates data following the diffusion tensor model
+Generates data following the diffusion tensor and/or kurtosis model and then fit with dtifit
+
+No noise is added, so we expect (near-)perfect fits
"""
import sys
import os
@@ -14,9 +16,13 @@ OUTDIR = sys.argv[0]
def gen_data():
"""
- Populates given directory with diffusion data
+ Populates given directory with diffusion data following DTI or DKI models
+
+ :yield: tuple with
- :yield: directories containing reference noiseless data with the eigen-vectors and eigen-values used to generate the data
+ - directory containing reference noiseless data with the eigen-vectors and eigen-values used to generate the data
+ - Boolean flag indicating whether data is multi-shell
+ - integer encoding diffusion model used (0: DTI, 1: single kurtosis value, 2: directional kurtosis)
"""
directory = [''] * 10
directory[0] = 'dti'
@@ -124,6 +130,21 @@ def gen_data():
def fit_data(directory):
+ """
+ Runs dtifit on the diffusion data multiple times with different flags
+
+ Tests with and without the following flags:
+
+ - --wls
+ - --kurt
+ - --kurtdir
+
+ :yield: tuple with
+
+ - base name of the output files
+ - boolean indicating whether the --kurt flag was set
+ - boolean indicating whether the --kudtdir flag was set
+ """
for kurtdir in (False, True):
for main_kurt in (False, True):
for wls in (False, True): # in this noise-free data the --wls flag should not matter
@@ -154,6 +175,7 @@ def fit_data(directory):
yield base_output, main_kurt, kurtdir
+# Loops through multiple ways to generate and fit the data and check the output
for directory, multi_shell, kurt in gen_data():
for base_output, fkurt, fkurtdir in fit_data(directory):
print('testing', base_output)
--
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