From 972fa85398c6dfde492d7437bbc50001db69d934 Mon Sep 17 00:00:00 2001
From: Dmitry Ganyushin <ganyushin@gmail.com>
Date: Wed, 3 Jul 2024 17:21:41 -0400
Subject: [PATCH] Converted test to python notebook example.

---
 notebooks/example_ms.ipynb    | 60 +++++++++++++++++++++++++++++++++++
 tests/scripts/denoise-gpu.py  | 46 ---------------------------
 tests/scripts/denoise-orig.py | 31 ------------------
 3 files changed, 60 insertions(+), 77 deletions(-)
 create mode 100644 notebooks/example_ms.ipynb
 delete mode 100644 tests/scripts/denoise-gpu.py
 delete mode 100644 tests/scripts/denoise-orig.py

diff --git a/notebooks/example_ms.ipynb b/notebooks/example_ms.ipynb
new file mode 100644
index 0000000..28f008e
--- /dev/null
+++ b/notebooks/example_ms.ipynb
@@ -0,0 +1,60 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import numpy as np\n",
+    "import matplotlib.pyplot as plt\n",
+    "from bm3dornl.bm3d import bm3d_ring_artifact_removal_ms\n",
+    "from bm3dornl.denoiser_gpu import memory_cleanup\n",
+    "\n",
+    "with open(\"../../tests/bm3dornl-data/sino.npy\", \"rb\") as f:\n",
+    "    sino_noisy = np.load(f)\n",
+    "\n",
+    "memory_cleanup()\n",
+    "\n",
+    "block_matching_kwargs: dict = {\n",
+    "    \"patch_size\": (8, 8),\n",
+    "    \"stride\": 3,\n",
+    "    \"background_threshold\": 0.0,\n",
+    "    \"cut_off_distance\": (64, 64),\n",
+    "    \"num_patches_per_group\": 32,\n",
+    "    \"padding_mode\": \"circular\",\n",
+    "}\n",
+    "filter_kwargs: dict = {\n",
+    "    \"filter_function\": \"fft\",\n",
+    "    \"shrinkage_factor\": 3e-2,\n",
+    "}\n",
+    "kwargs = {\n",
+    "    \"mode\": \"simple\",\n",
+    "    \"k\": 4,\n",
+    "    \"block_matching_kwargs\": block_matching_kwargs,\n",
+    "    \"filter_kwargs\": filter_kwargs,\n",
+    "}\n",
+    "\n",
+    "sino_bm3dornl = bm3d_ring_artifact_removal_ms(\n",
+    "    sinogram=sino_noisy,\n",
+    "    **kwargs,\n",
+    ")\n",
+    "\n",
+    "\n",
+    "fig, axs = plt.subplots(1, 2, figsize=(12, 4))\n",
+    "axs[0].imshow(sino_noisy, cmap=\"gray\")\n",
+    "axs[0].set_title(\"Noisy sinogram\")\n",
+    "axs[1].imshow(sino_bm3dornl, cmap=\"gray\")\n",
+    "axs[1].set_title(\"BM3D denoised sinogram\")\n",
+    "plt.show()\n"
+   ]
+  }
+ ],
+ "metadata": {
+  "language_info": {
+   "name": "python"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}
diff --git a/tests/scripts/denoise-gpu.py b/tests/scripts/denoise-gpu.py
deleted file mode 100644
index ddb0b29..0000000
--- a/tests/scripts/denoise-gpu.py
+++ /dev/null
@@ -1,46 +0,0 @@
-import numpy as np
-import matplotlib.pyplot as plt
-from bm3dornl.bm3d import bm3d_ring_artifact_removal_ms
-from bm3dornl.denoiser_gpu import memory_cleanup
-
-print("Reading sinogram from file ...")
-with open("../bm3dornl-data/sino.npy", "rb") as f:
-    sino_noisy = np.load(f)
-
-print("done")
-
-memory_cleanup()
-
-block_matching_kwargs: dict = {
-    "patch_size": (8, 8),
-    "stride": 3,
-    "background_threshold": 0.0,
-    "cut_off_distance": (64, 64),
-    "num_patches_per_group": 32,
-    "padding_mode": "circular",
-}
-filter_kwargs: dict = {
-    "filter_function": "fft",
-    "shrinkage_factor": 3e-2,
-}
-kwargs = {
-    "mode": "simple",
-    "k": 4,
-    "block_matching_kwargs": block_matching_kwargs,
-    "filter_kwargs": filter_kwargs,
-}
-
-sino_bm3dornl = bm3d_ring_artifact_removal_ms(
-    sinogram=sino_noisy,
-    **kwargs,
-)
-
-
-fig, axs = plt.subplots(1, 2, figsize=(12, 4))
-axs[0].imshow(sino_noisy, cmap="gray")
-axs[0].set_title("Noisy sinogram")
-axs[1].imshow(sino_bm3dornl, cmap="gray")
-axs[1].set_title("BM3D denoised sinogram")
-# plt.show()
-fig.savefig("denoise-gpu.png")
-plt.close(fig)
diff --git a/tests/scripts/denoise-orig.py b/tests/scripts/denoise-orig.py
deleted file mode 100644
index 20b366a..0000000
--- a/tests/scripts/denoise-orig.py
+++ /dev/null
@@ -1,31 +0,0 @@
-import numpy as np
-import matplotlib.pyplot as plt
-import bm3d_streak_removal as bm3dsr
-
-print("Reading sinogram from file ...")
-
-with open("../bm3dornl-data/sino.npy", "rb") as f:
-    sino_noisy = np.load(f)
-
-print("done")
-
-sino_bm3d = bm3dsr.multiscale_streak_removal(
-    data=sino_noisy,
-    max_bin_iter_horizontal=0,
-    bin_vertical=0,
-    filter_strength=1.0,
-    use_slices=True,
-    slice_sizes=None,
-    slice_step_sizes=None,
-    denoise_indices=None,
-)
-
-
-fig, axs = plt.subplots(1, 2, figsize=(12, 4))
-axs[0].imshow(sino_noisy, cmap="gray")
-axs[0].set_title("Noisy sinogram")
-axs[1].imshow(sino_bm3d, cmap="gray")
-axs[1].set_title("BM3D denoised sinogram")
-# plt.show()
-fig.savefig("denoise-orig.png")
-plt.close(fig)