Merge branch 'main' into zenodo_IO

OSIPI · Mar 6, 2024 · b7417e6 · b7417e6
2 parents 0801ec3 + 1f4cbf4
commit b7417e6
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diff --git a/.github/workflows/analysis.yml b/.github/workflows/analysis.yml
@@ -12,10 +12,10 @@ jobs:
     outputs: # here we use the outputs from steps, and set outputs for the job `configure`
       algorithms: ${{ steps.algorithms.outputs.algorithms }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python
         id: setup_python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: "3.11"
           cache: 'pip'
@@ -53,9 +53,9 @@ jobs:
         algorithm: ${{fromJson(needs.algorithms.outputs.algorithms).algorithms}}
         SNR: [10, 30, 50, 100, 200]
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: "3.11"
           cache: 'pip'
@@ -111,7 +111,7 @@ jobs:
     runs-on: ubuntu-latest
     needs: merge
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up R
         uses: r-lib/actions/setup-r@v2
         with: 
@@ -151,7 +151,7 @@ jobs:
     runs-on: ubuntu-latest
     needs: merge
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up R
         uses: r-lib/actions/setup-r@v2
         with: 
@@ -175,4 +175,4 @@ jobs:
             name: Comparison
             path: |
               test_reference.csv
-              test_results.csv
+              test_results.csv
diff --git a/.github/workflows/unit_test.yml b/.github/workflows/unit_test.yml
@@ -18,9 +18,9 @@ jobs:
         #   - os: windows-latest
         #     python-version: "3.7"
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
           cache: 'pip'

diff --git a/requirements.txt b/requirements.txt
@@ -8,4 +8,6 @@ dipy
 matplotlib
 scienceplots
 cvxpy
-zenodo-get
+zenodo-get
+pytest
+tqdm
diff --git a/src/original/TCML_TechnionIIT/SUPER-IVIM-DC/README.md b/src/original/TCML_TechnionIIT/SUPER-IVIM-DC/README.md
@@ -0,0 +1,21 @@
+# SUPER-IVIM-DC
+
+Provided here is a sample Jupyter notebook for the SUPER-IVIM-DC package.
+
+Full README and usage instructions can be found here: https://github.com/TechnionComputationalMRILab/SUPER-IVIM-DC or https://pypi.org/project/super-ivim-dc/0.4.0/
+
+Citation: 
+
+```
+@article{
+  Korngut_Rotman_Afacan_Kurugol_Zaffrani-Reznikov_Nemirovsky-Rotman_Warfield_Freiman_2022,
+  title={SUPER-IVIM-DC: Intra-voxel incoherent motion based fetal lung maturity assessment from limited DWI data using supervised learning coupled with data-consistency},
+  volume={13432}, DOI={10.1007/978-3-031-16434-7_71},
+  journal={Lecture Notes in Computer Science},
+  author={Korngut, Noam and Rotman, Elad and Afacan, Onur and Kurugol, Sila and Zaffrani-Reznikov, Yael and Nemirovsky-Rotman, Shira and Warfield, Simon and Freiman, Moti},
+  year={2022},
+  pages={743–752}
+}
+```
+
+[The paper is also available on ArXiv](https://arxiv.org/abs/2206.03820).
diff --git a/src/original/TCML_TechnionIIT/SUPER-IVIM-DC/sample.ipynb b/src/original/TCML_TechnionIIT/SUPER-IVIM-DC/sample.ipynb
@@ -0,0 +1,167 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import numpy as np\n",
+    "working_dir: str = './working_dir'\n",
+    "super_ivim_dc_filename: str = 'super_ivim_dc'  # do not include .pt\n",
+    "ivimnet_filename: str = 'ivimnet'  # do not include .pt\n",
+    "\n",
+    "bvalues = np.array([0,15,30,45,60,75,90,105,120,135,150,175,200,400,600,800])\n",
+    "snr = 10\n",
+    "sample_size = 100"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Simulate"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Run training, generate .pt files"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from super_ivim_dc.train import train\n",
+    "\n",
+    "train(\n",
+    "    SNR=snr, \n",
+    "    bvalues=bvalues, \n",
+    "    super_ivim_dc=True,\n",
+    "    ivimnet=True,\n",
+    "    work_dir=working_dir,\n",
+    "    super_ivim_dc_filename=super_ivim_dc_filename,\n",
+    "    ivimnet_filename=ivimnet_filename,\n",
+    "    verbose=False\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Files that will be created:\n",
+    "\n",
+    "- **super_ivim_dc_init.json** - contains the initial values used in the training\n",
+    "- **super_ivim_dc_init_NRMSE.csv** - ???\n",
+    "- **super_ivim_dc_init.pt** - the pytorch model"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Test\n",
+    "\n",
+    "Generate a simulated signal + ..."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from super_ivim_dc.infer import test_infer\n",
+    "\n",
+    "test_infer(\n",
+    "    SNR=snr,\n",
+    "    bvalues=bvalues,\n",
+    "    work_dir=working_dir,\n",
+    "    super_ivim_dc_filename=super_ivim_dc_filename,\n",
+    "    ivimnet_filename=ivimnet_filename,\n",
+    "    save_figure_to=None,  # if set to None, the figure will be shown in the notebook\n",
+    "    sample_size=sample_size,\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Generate simulated signal"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from super_ivim_dc.IVIMNET import simulations\n",
+    "\n",
+    "IVIM_signal_noisy, Dt, f, Dp = simulations.sim_signal(\n",
+    "    SNR=snr, \n",
+    "    bvalues=bvalues, \n",
+    "    sims=sample_size\n",
+    ")\n",
+    "\n",
+    "Dt, f, Dp = np.squeeze(Dt), np.squeeze(f), np.squeeze(Dp)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Run inference on the simulated signal"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from super_ivim_dc.infer import infer_from_signal\n",
+    "\n",
+    "Dp_ivimnet, Dt_ivimnet, Fp_ivimnet, S0_ivimnet = infer_from_signal(\n",
+    "    signal=IVIM_signal_noisy, \n",
+    "    bvalues=bvalues,\n",
+    "    model_path=f\"{working_dir}/{ivimnet_filename}.pt\",\n",
+    ")\n",
+    "\n",
+    "Dp_superivimdc, Dt_superivimdc, Fp_superivimdc, S0_superivimdc = infer_from_signal(\n",
+    "    signal=IVIM_signal_noisy, \n",
+    "    bvalues=bvalues,\n",
+    "    model_path=f\"{working_dir}/{super_ivim_dc_filename}.pt\",\n",
+    ")"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "super_ivim_dc",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.12"
+  },
+  "orig_nbformat": 4
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}