Merge pull request #8 from mjt320/develop

prepared for distribution
mjt320 · Feb 7, 2024 · 524d6e5 · 524d6e5
2 parents ced76cc + 54c96d9
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diff --git a/.idea/SEPAL.iml b/.idea/SEPAL.iml
diff --git a/.idea/misc.xml b/.idea/misc.xml
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -0,0 +1,4 @@
+# MANIFEST.in
+
+recursive-include demo *
+prune demo/.ipynb_checkpoints
diff --git a/README.md b/README.md
@@ -1,14 +1,20 @@
-# South Edinburgh Perfusion Analysis Library (SEPAL)
+# South Edinburgh Perfusion+ Analysis Library (SEPAL)
 
 **Please note: This library is also hosted in the [OSIPI DCE-DSC-MRI_CodeCollection repository](https://github.com/OSIPI/DCE-DSC-MRI_CodeCollection), where unit tests and perfusion code by other authors can also be found.**
 
-Python library for simulating and fitting DCE-MRI data. It permits arbitrary combinations of pulse sequence, pharmacokinetic model, water exchange model, etc. The code is a work-in-progress, has not been extensively tested and is not recommended or approved for clinical use.
+Python library for simulating and fitting DCE- and other quantitative MRI data. It permits arbitrary combinations of pulse sequence, pharmacokinetic model, water exchange model, etc. The code is a work-in-progress, has not been extensively tested and is not recommended or approved for clinical use.
 
 Created 28 September 2020  
 @authors: Michael Thrippleton  
 @email: [email protected]  
 @institution: University of Edinburgh, UK
 
+### Installation:
+pip install sepal
+
+### Use:
+Most functionality is demonstrated in Jupyter notebook format in ./demo 
+
 ### Functionality:
 - Enhancement-to-concentration conversion (assuming fast water exchange)
 - Fit tissue concentration using pharmacokinetic model

diff --git a/demo/demo_aif_module.ipynb b/demo/demo_aif_module.ipynb
diff --git a/demo/demo_enh_to_conc.ipynb b/demo/demo_enh_to_conc.ipynb
diff --git a/demo/demo_fit_dce.ipynb b/demo/demo_fit_dce.ipynb
diff --git a/demo/demo_fit_t1.ipynb b/demo/demo_fit_t1.ipynb
diff --git a/demo/demo_fit_t2s.ipynb b/demo/demo_fit_t2s.ipynb
diff --git a/demo/demo_imaging_utilities.ipynb b/demo/demo_imaging_utilities.ipynb
diff --git a/demo/demo_mt.ipynb b/demo/demo_mt.ipynb
diff --git a/demo/demo_pk_models.ipynb b/demo/demo_pk_models.ipynb
diff --git a/demo/demo_relaxivity_module.ipynb b/demo/demo_relaxivity_module.ipynb
@@ -3,40 +3,40 @@
   {
    "cell_type": "markdown",
    "id": "fifty-passport",
-   "metadata": {},
+   "metadata": {
+    "pycharm": {
+     "name": "#%% md\n"
+    }
+   },
    "source": [
     "## Relaxivity module demo"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 1,
    "id": "internal-arbor",
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "The autoreload extension is already loaded. To reload it, use:\n",
-      "  %reload_ext autoreload\n"
-     ]
+   "metadata": {
+    "pycharm": {
+     "name": "#%%\n"
     }
-   ],
+   },
+   "outputs": [],
    "source": [
-    "import sys\n",
-    "import matplotlib.pyplot as plt\n",
     "import numpy as np\n",
-    "sys.path.append('../src')\n",
-    "import relaxivity\n",
+    "from sepal import relaxivity\n",
     "%load_ext autoreload\n",
     "%autoreload 2"
    ]
   },
   {
    "cell_type": "markdown",
    "id": "arabic-latvia",
-   "metadata": {},
+   "metadata": {
+    "pycharm": {
+     "name": "#%% md\n"
+    }
+   },
    "source": [
     "### The CRModel class\n",
     "This is an abstract base class. Subclasses represent specific relaxivity models.  \n",
@@ -46,9 +46,13 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 2,
    "id": "4080ceab-24f8-4b2e-b57d-816474887489",
-   "metadata": {},
+   "metadata": {
+    "pycharm": {
+     "name": "#%%\n"
+    }
+   },
    "outputs": [],
    "source": [
     "cr_model = relaxivity.CRLinear(r1=5.0, r2=7.1)"
@@ -57,16 +61,24 @@
   {
    "cell_type": "markdown",
    "id": "52762d06-81e5-4153-88f5-5d0e827d7f82",
-   "metadata": {},
+   "metadata": {
+    "pycharm": {
+     "name": "#%% md\n"
+    }
+   },
    "source": [
     "Now we can use the R1 and R2 methods to calculate the relaxation rates for a given concentration and pre-contrast relaxation rate values:"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 3,
    "id": "a3c01c12-fb5e-4aed-b9fb-b882270ba27f",
-   "metadata": {},
+   "metadata": {
+    "pycharm": {
+     "name": "#%%\n"
+    }
+   },
    "outputs": [
     {
      "name": "stdout",
@@ -86,7 +98,11 @@
   {
    "cell_type": "markdown",
    "id": "4a7c1681-7e9d-49b2-9474-56f86a8f25ef",
-   "metadata": {},
+   "metadata": {
+    "pycharm": {
+     "name": "#%% md\n"
+    }
+   },
    "source": [
     "Additional subclasses could be implemented to represent other concentration-relaxation relationships, e.g. quadratic."
    ]
@@ -113,4 +129,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 5
-}
+}
diff --git a/demo/demo_signal_models.ipynb b/demo/demo_signal_models.ipynb
diff --git a/demo/demo_simulation.ipynb b/demo/demo_simulation.ipynb
diff --git a/demo/demo_water_ex_models.ipynb b/demo/demo_water_ex_models.ipynb
@@ -3,7 +3,11 @@
   {
    "cell_type": "markdown",
    "id": "eb332c7d-4589-47da-81d0-e2697ee70254",
-   "metadata": {},
+   "metadata": {
+    "pycharm": {
+     "name": "#%% md\n"
+    }
+   },
    "source": [
     "## Water exchange models demo"
    ]
@@ -13,23 +17,26 @@
    "execution_count": 1,
    "id": "42671502-6096-4107-8c21-3f876b950a66",
    "metadata": {
-    "tags": []
+    "tags": [],
+    "pycharm": {
+     "name": "#%%\n"
+    }
    },
    "outputs": [],
    "source": [
-    "import sys\n",
-    "import matplotlib.pyplot as plt\n",
-    "import numpy as np\n",
-    "sys.path.append('../src')\n",
-    "import water_ex_models\n",
+    "from sepal import water_ex_models\n",
     "%load_ext autoreload\n",
     "%autoreload 2"
    ]
   },
   {
    "cell_type": "markdown",
    "id": "33acaa3b-10e0-454f-b62b-6a2cb5b1d0f4",
-   "metadata": {},
+   "metadata": {
+    "pycharm": {
+     "name": "#%% md\n"
+    }
+   },
    "source": [
     "### The WaterExModel Class\n",
     "This abstract base class represents different water exchange models. The purpose of such an object is to convert a set of relaxation rates for each tissue compartment (blood, EES, cells) into one or more exponential relaxation components based on the water exchange properties.  \n",
@@ -38,9 +45,13 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 2,
    "id": "c2e14ed8-c6f6-4e79-9fe0-fbc9b323d156",
-   "metadata": {},
+   "metadata": {
+    "pycharm": {
+     "name": "#%%\n"
+    }
+   },
    "outputs": [],
    "source": [
     "p = {'b': 0.2, 'e': 0.4, 'i': 0.4}\n",
@@ -50,17 +61,25 @@
   {
    "cell_type": "markdown",
    "id": "b6b07fe1-e732-4e57-9c4f-857815a6de3b",
-   "metadata": {},
+   "metadata": {
+    "pycharm": {
+     "name": "#%% md\n"
+    }
+   },
    "source": [
     "#### FXL\n",
     "In the FXL, we end up with just one longitudinal relaxation component representing the tissue:"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 3,
    "id": "29c9d0d4-3fc0-44f5-ba00-322339389d8f",
-   "metadata": {},
+   "metadata": {
+    "pycharm": {
+     "name": "#%%\n"
+    }
+   },
    "outputs": [
     {
      "name": "stdout",
@@ -81,17 +100,25 @@
   {
    "cell_type": "markdown",
    "id": "e7855797-9f25-4ef3-b04e-6dd87d78169e",
-   "metadata": {},
+   "metadata": {
+    "pycharm": {
+     "name": "#%% md\n"
+    }
+   },
    "source": [
     "#### NXL\n",
     "In the NXL, we get 3 relaxation components corresponding to the 3 tissue compartments:"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 4,
    "id": "0e547b96-a11b-48aa-88fd-99f46638c8f3",
-   "metadata": {},
+   "metadata": {
+    "pycharm": {
+     "name": "#%%\n"
+    }
+   },
    "outputs": [
     {
      "name": "stdout",
@@ -112,17 +139,25 @@
   {
    "cell_type": "markdown",
    "id": "db686624-a214-45e2-bae1-4e173f076d3f",
-   "metadata": {},
+   "metadata": {
+    "pycharm": {
+     "name": "#%% md\n"
+    }
+   },
    "source": [
     "#### NTEXL\n",
     "In the No-TransEndothelial-water-eXchange Limit, we get relaxation components corresponding to blood and the combined extravascular spaces:"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 5,
    "id": "feaf0f84-b3c9-44ee-ae22-7144cdd59e8b",
-   "metadata": {},
+   "metadata": {
+    "pycharm": {
+     "name": "#%%\n"
+    }
+   },
    "outputs": [
     {
      "name": "stdout",
@@ -143,7 +178,11 @@
   {
    "cell_type": "markdown",
    "id": "867ae4b1-5486-46c0-b2f8-5c73efdb0d29",
-   "metadata": {},
+   "metadata": {
+    "pycharm": {
+     "name": "#%% md\n"
+    }
+   },
    "source": [
     "#### Other water exchange models\n",
     "Other models could be added, e.g. 3-site-2-exchange, 2-site-1-exchange."
@@ -171,4 +210,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 5
-}
+}
diff --git a/pyproject.toml b/pyproject.toml
@@ -0,0 +1,29 @@
+# pyproject.toml
+
+[build-system]
+requires = ["setuptools>=61.0.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "sepal"
+version = "1.0.0"
+description = "Quantitative MRI processing"
+readme = "README.md"
+authors = [{ name = "Michael Thrippleton", email = "[email protected]" }]
+license = { file = "LICENSE" }
+classifiers = [
+    "License :: OSI Approved :: Apache Software License",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+]
+keywords = ["MRI", "perfusion", "quantitative"]
+dependencies = [
+    "numpy",
+    "scipy",
+    "nibabel",
+    "joblib",
+]
+requires-python = ">=3.7"
+
+[project.urls]
+Homepage = "https://github.com/mjt320/SEPAL"
diff --git a/setup.py b/setup.py
@@ -0,0 +1,5 @@
+# setup.py
+
+from setuptools import setup
+
+setup()
diff --git a/src/__init__.py → src/sepal/__init__.py b/src/__init__.py → src/sepal/__init__.py
diff --git a/src/aifs.py → src/sepal/aifs.py b/src/aifs.py → src/sepal/aifs.py
diff --git a/src/dce_fit.py → src/sepal/dce_fit.py b/src/dce_fit.py → src/sepal/dce_fit.py
@@ -23,9 +23,9 @@
 import numpy as np
 from scipy.signal import argrelextrema
 from scipy.interpolate import interp1d
-from fitting import Fitter
-from pk_models import Patlak
-from utils.utilities import least_squares_global
+from sepal.fitting import Fitter
+from sepal.pk_models import Patlak
+from sepal.utils.utilities import least_squares_global
 
 
 class SigToEnh(Fitter):