From 3ab2279c65fdd6bcb9967028c09dc1475e14065e Mon Sep 17 00:00:00 2001
From: haesleinhuepf <rhaase@mpi-cbg.de>
Date: Tue, 23 Jun 2020 13:05:50 +0200
Subject: [PATCH] added another potential solution (which is not working)
---
.../Otsu_Method_Comparison.ipynb | 106 ++++++++++++++++--
1 file changed, 95 insertions(+), 11 deletions(-)
diff --git a/11_Hypothesis_testing/exercise_otsu/Otsu_Method_Comparison.ipynb b/11_Hypothesis_testing/exercise_otsu/Otsu_Method_Comparison.ipynb
index 73e1e95..025f5e6 100644
--- a/11_Hypothesis_testing/exercise_otsu/Otsu_Method_Comparison.ipynb
+++ b/11_Hypothesis_testing/exercise_otsu/Otsu_Method_Comparison.ipynb
@@ -2,7 +2,7 @@
"cells": [
{
"cell_type": "code",
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+ "execution_count": 1,
"metadata": {},
"outputs": [
{
@@ -88,7 +88,7 @@
},
{
"cell_type": "code",
- "execution_count": 3,
+ "execution_count": 2,
"metadata": {},
"outputs": [
{
@@ -123,7 +123,7 @@
},
{
"cell_type": "code",
- "execution_count": 4,
+ "execution_count": 3,
"metadata": {},
"outputs": [
{
@@ -174,7 +174,7 @@
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{
"cell_type": "code",
- "execution_count": 5,
+ "execution_count": 4,
"metadata": {},
"outputs": [
{
@@ -209,7 +209,7 @@
},
{
"cell_type": "code",
- "execution_count": 6,
+ "execution_count": 5,
"metadata": {},
"outputs": [],
"source": [
@@ -234,7 +234,7 @@
},
{
"cell_type": "code",
- "execution_count": 7,
+ "execution_count": 6,
"metadata": {},
"outputs": [
{
@@ -265,7 +265,7 @@
},
{
"cell_type": "code",
- "execution_count": 8,
+ "execution_count": 7,
"metadata": {},
"outputs": [
{
@@ -292,7 +292,7 @@
},
{
"cell_type": "code",
- "execution_count": 41,
+ "execution_count": 8,
"metadata": {},
"outputs": [
{
@@ -303,7 +303,7 @@
" (-0.0743754713943518, 0.47051036223078757, 48.0))"
]
},
- "execution_count": 41,
+ "execution_count": 8,
"metadata": {},
"output_type": "execute_result"
}
@@ -318,7 +318,91 @@
},
{
"cell_type": "code",
- "execution_count": 40,
+ "execution_count": 9,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# source: https://gist.github.com/josef-pkt/3900314\n",
+ "\n",
+ "'''Test of Equivalence and Non-Inferiority\n",
+ "currently only TOST for paired sample\n",
+ "Application for example bioequivalence\n",
+ "Author: Josef Perktold\n",
+ "License: BSD-3\n",
+ "'''\n",
+ "\n",
+ "\n",
+ "import numpy as np\n",
+ "from scipy import stats\n",
+ "\n",
+ "def tost_paired(y, x, low, upp, transform=None):\n",
+ " '''test of (non-)equivalence for paired sample\n",
+ " TOST: two one-sided t tests\n",
+ " null hypothesis x - y < low or x - y > upp\n",
+ " alternative hypothesis: low < x - y < upp\n",
+ " If the pvalue is smaller than a threshold, then we reject the hypothesis\n",
+ " that there is difference between the two samples larger than the one\n",
+ " given by low and upp.\n",
+ " Parameters\n",
+ " ----------\n",
+ " y, x : array_like\n",
+ " two paired samples\n",
+ " low, upp : float\n",
+ " equivalence interval low < x - y < upp\n",
+ " transform : None or function\n",
+ " If None (default), then the data is not transformed. Given a function\n",
+ " sample data and thresholds are transformed. If transform is log the\n",
+ " the equivalence interval is in ratio: low < x / y < upp\n",
+ " Returns\n",
+ " -------\n",
+ " pvalue : float\n",
+ " pvalue of the non-equivalence test\n",
+ " t1, pv1 : tuple of floats\n",
+ " test statistic and pvalue for lower threshold test\n",
+ " t2, pv2 : tuple of floats\n",
+ " test statistic and pvalue for upper threshold test\n",
+ " Notes\n",
+ " -----\n",
+ " tested on only one example\n",
+ " uses stats.ttest_1samp which doesn't have a real one-sided option\n",
+ " '''\n",
+ " if transform:\n",
+ " y = transform(y)\n",
+ " x = transform(x)\n",
+ " low = transform(low)\n",
+ " upp = transform(upp)\n",
+ " t1, pv1 = stats.ttest_1samp(x - y, low)\n",
+ " t2, pv2 = stats.ttest_1samp(x - y, upp)\n",
+ " return max(pv1, pv2)/2., (t1, pv1 / 2.), (t2, pv2 / 2.)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 10,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "(3.0607159809231846e-11,\n",
+ " (-11.104032129950907, 3.0607159809231846e-11),\n",
+ " (-12.32257205021279, 3.601584280854005e-12))"
+ ]
+ },
+ "execution_count": 10,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "tolerance = 0.1\n",
+ "\n",
+ "tost_paired(measurement_python, measurement_imagej, -tolerance, tolerance)\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 11,
"metadata": {},
"outputs": [
{
@@ -336,7 +420,7 @@
" [72.64029810317597, 1.19906617345889e-29]]"
]
},
- "execution_count": 40,
+ "execution_count": 11,
"metadata": {},
"output_type": "execute_result"
}
--
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