diff --git a/.idea/SEPAL.iml b/.idea/SEPAL.iml
index d49a298..4606b2f 100644
--- a/.idea/SEPAL.iml
+++ b/.idea/SEPAL.iml
@@ -11,5 +11,6 @@
+
\ No newline at end of file
diff --git a/.idea/other.xml b/.idea/other.xml
new file mode 100644
index 0000000..640fd80
--- /dev/null
+++ b/.idea/other.xml
@@ -0,0 +1,7 @@
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/demo/demo_aif_module.ipynb b/demo/demo_aif_module.ipynb
index 8fcecee..4a23fa7 100644
--- a/demo/demo_aif_module.ipynb
+++ b/demo/demo_aif_module.ipynb
@@ -3,7 +3,11 @@
{
"cell_type": "markdown",
"id": "eb332c7d-4589-47da-81d0-e2697ee70254",
- "metadata": {},
+ "metadata": {
+ "pycharm": {
+ "name": "#%% md\n"
+ }
+ },
"source": [
"## AIF module demo"
]
@@ -11,7 +15,11 @@
{
"cell_type": "markdown",
"id": "4276273d-31f5-4625-bfc8-9018b7cd984d",
- "metadata": {},
+ "metadata": {
+ "pycharm": {
+ "name": "#%% md\n"
+ }
+ },
"source": [
"### Import modules"
]
@@ -21,7 +29,10 @@
"execution_count": 2,
"id": "42671502-6096-4107-8c21-3f876b950a66",
"metadata": {
- "tags": []
+ "tags": [],
+ "pycharm": {
+ "name": "#%%\n"
+ }
},
"outputs": [
{
@@ -46,7 +57,11 @@
{
"cell_type": "markdown",
"id": "0c2eae34-da30-465b-9b23-3dbadd7dc0d8",
- "metadata": {},
+ "metadata": {
+ "pycharm": {
+ "name": "#%% md\n"
+ }
+ },
"source": [
"### The AIF Class\n",
"AIF objects define an arterial input function. This can either be a population average function or an AIF based on individual patient measurements."
@@ -55,7 +70,11 @@
{
"cell_type": "markdown",
"id": "reported-projector",
- "metadata": {},
+ "metadata": {
+ "pycharm": {
+ "name": "#%% md\n"
+ }
+ },
"source": [
"### Classic Parker AIF\n",
"Create a Parker AIF object of the Parker subclass of AIF:"
@@ -65,7 +84,11 @@
"cell_type": "code",
"execution_count": 3,
"id": "4f59a6a6-69b0-4f28-a4a1-03b0b846f6e8",
- "metadata": {},
+ "metadata": {
+ "pycharm": {
+ "name": "#%%\n"
+ }
+ },
"outputs": [],
"source": [
"parker_aif = aifs.Parker(hct=0.42)"
@@ -74,7 +97,11 @@
{
"cell_type": "markdown",
"id": "f9a0f8e5-ddd6-4164-a4df-7f50a3af82eb",
- "metadata": {},
+ "metadata": {
+ "pycharm": {
+ "name": "#%% md\n"
+ }
+ },
"source": [
"We can use the c_ap method to get concentration at arbitrary time points:"
]
@@ -83,7 +110,11 @@
"cell_type": "code",
"execution_count": 4,
"id": "f65ca4cc-58d3-422a-822b-6c52cd9328c9",
- "metadata": {},
+ "metadata": {
+ "pycharm": {
+ "name": "#%%\n"
+ }
+ },
"outputs": [
{
"data": {
@@ -110,7 +141,11 @@
{
"cell_type": "markdown",
"id": "electoral-tamil",
- "metadata": {},
+ "metadata": {
+ "pycharm": {
+ "name": "#%% md\n"
+ }
+ },
"source": [
"### Patient-specific AIF\n",
"Now we create an individual AIF object based on a series of time-concentration data points. We use the PatientSpecific subclass of AIF."
@@ -120,7 +155,11 @@
"cell_type": "code",
"execution_count": 5,
"id": "2d0a1c5b-7972-4be9-aa1b-9029e5645685",
- "metadata": {},
+ "metadata": {
+ "pycharm": {
+ "name": "#%%\n"
+ }
+ },
"outputs": [],
"source": [
"t_patient = np.array([19.810000,59.430000,99.050000,138.670000,178.290000,217.910000,257.530000,297.150000,336.770000,376.390000,416.010000,455.630000,495.250000,534.870000,574.490000,614.110000,653.730000,693.350000,732.970000,772.590000,812.210000,851.830000,891.450000,931.070000,970.690000,1010.310000,1049.930000,1089.550000,1129.170000,1168.790000,1208.410000,1248.030000])\n",
@@ -132,7 +171,11 @@
{
"cell_type": "markdown",
"id": "9a03a459-93d7-4779-9709-6389bf265024",
- "metadata": {},
+ "metadata": {
+ "pycharm": {
+ "name": "#%% md\n"
+ }
+ },
"source": [
"Again, using the c_ap method we can get concentration at arbitrary time points. This is achieved using interpolation function."
]
@@ -141,7 +184,11 @@
"cell_type": "code",
"execution_count": 6,
"id": "c9d16286-d0df-4ab8-b918-4486652200f0",
- "metadata": {},
+ "metadata": {
+ "pycharm": {
+ "name": "#%%\n"
+ }
+ },
"outputs": [
{
"data": {
@@ -176,7 +223,11 @@
{
"cell_type": "markdown",
"id": "d30c7325-3453-4e38-a869-7439ed256437",
- "metadata": {},
+ "metadata": {
+ "pycharm": {
+ "name": "#%% md\n"
+ }
+ },
"source": [
"### Other standard AIF functions\n",
"The following function is described in Manning et al., Magn Reson Med. 2021;86:1888–1903. \n",
@@ -188,7 +239,11 @@
"cell_type": "code",
"execution_count": 7,
"id": "e7274fdd-ef51-40fd-8ce9-d1b2820aa37e",
- "metadata": {},
+ "metadata": {
+ "pycharm": {
+ "name": "#%%\n"
+ }
+ },
"outputs": [],
"source": [
"manning_fast_aif = aifs.ManningFast(hct=0.42, t_start=3*39.62)"
@@ -197,7 +252,11 @@
{
"cell_type": "markdown",
"id": "83da4ffa-24c2-4e24-b1ec-30ed89a823c2",
- "metadata": {},
+ "metadata": {
+ "pycharm": {
+ "name": "#%% md\n"
+ }
+ },
"source": [
"Manning et al. also reports an AIF for *slow* contrast injections in the same patient population, based on patient measurements:"
]
@@ -206,7 +265,11 @@
"cell_type": "code",
"execution_count": 8,
"id": "a9cd6fa3-3347-4c4d-9cc4-da0d2d027c69",
- "metadata": {},
+ "metadata": {
+ "pycharm": {
+ "name": "#%%\n"
+ }
+ },
"outputs": [],
"source": [
"manning_slow_aif = aifs.ManningSlow()"
@@ -215,7 +278,11 @@
{
"cell_type": "markdown",
"id": "f3d27241-b579-4b38-9ecd-1658184e6253",
- "metadata": {},
+ "metadata": {
+ "pycharm": {
+ "name": "#%% md\n"
+ }
+ },
"source": [
"A similar population average function (for Bolus injection) was reported in Heye et al., NeuroImage 2016;125:446-455:"
]
@@ -224,7 +291,11 @@
"cell_type": "code",
"execution_count": 9,
"id": "a3fb3120-0b2c-420b-9e1f-0625ab9a4fff",
- "metadata": {},
+ "metadata": {
+ "pycharm": {
+ "name": "#%%\n"
+ }
+ },
"outputs": [],
"source": [
"heye_aif = aifs.Heye(hct=0.45, t_start=3*39.62)"
@@ -233,7 +304,11 @@
{
"cell_type": "markdown",
"id": "65d7c712-3ef0-4f87-a7b1-2dfa03c0e45d",
- "metadata": {},
+ "metadata": {
+ "pycharm": {
+ "name": "#%% md\n"
+ }
+ },
"source": [
"Plot the above AIFs (and the original Parker model) for comparison:"
]
@@ -242,7 +317,11 @@
"cell_type": "code",
"execution_count": 11,
"id": "f7d24797-32ac-467d-8ea8-66b24079fa49",
- "metadata": {},
+ "metadata": {
+ "pycharm": {
+ "name": "#%%\n"
+ }
+ },
"outputs": [
{
"data": {
@@ -293,4 +372,4 @@
},
"nbformat": 4,
"nbformat_minor": 5
-}
+}
\ No newline at end of file
diff --git a/demo/demo_conc_to_enh.ipynb b/demo/demo_conc_to_enh.ipynb
deleted file mode 100644
index 0d467fc..0000000
--- a/demo/demo_conc_to_enh.ipynb
+++ /dev/null
@@ -1,100 +0,0 @@
-{
- "cells": [
- {
- "cell_type": "code",
- "execution_count": 34,
- "id": "3b2d4aa7-5b11-44fc-ad48-069caaeab47a",
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "The autoreload extension is already loaded. To reload it, use:\n",
- " %reload_ext autoreload\n"
- ]
- }
- ],
- "source": [
- "import sys\n",
- "import matplotlib.pyplot as plt\n",
- "import numpy as np\n",
- "sys.path.append('../src')\n",
- "import dce_fit, relaxivity, signal_models, water_ex_models, aifs, pk_models\n",
- "%load_ext autoreload\n",
- "%autoreload 2"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 41,
- "id": "9439e538-cdd8-4849-bedf-1ead532f0811",
- "metadata": {},
- "outputs": [
- {
- "data": {
- "text/plain": [
- "[,\n",
- " ]"
- ]
- },
- "execution_count": 41,
- "metadata": {},
- "output_type": "execute_result"
- },
- {
- "data": {
- "image/png": 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\n",
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