From 94afc587dfa8fbb074e71778f495a19189604475 Mon Sep 17 00:00:00 2001
From: Eric Chen <85866693+EricVibration@users.noreply.github.com>
Date: Thu, 22 Sep 2022 13:19:55 +0900
Subject: [PATCH] Update Class
---
cell_wall_deformation_analysis.ipynb | 491 ++----------------
common/cell_wall_deformation_analysis_func.py | 340 ++++++++----
common/kmeans_clustering_func.py | 237 ++++-----
kmeans_clustering.ipynb | 46 +-
4 files changed, 437 insertions(+), 677 deletions(-)
diff --git a/cell_wall_deformation_analysis.ipynb b/cell_wall_deformation_analysis.ipynb
index 2c0d892..8267fda 100644
--- a/cell_wall_deformation_analysis.ipynb
+++ b/cell_wall_deformation_analysis.ipynb
@@ -5,8 +5,7 @@
"id": "b116f416-3c0d-4667-9458-2a630a8ef048",
"metadata": {},
"source": [
- "# Analysis cell wall defomration\n",
- "- it is an example for the submitted paper to construction and building materials"
+ "# Analyze cell wall deformation"
]
},
{
@@ -22,28 +21,6 @@
{
"cell_type": "code",
"execution_count": 2,
- "id": "bb028e46-3665-425b-8788-3cfb76122d7b",
- "metadata": {},
- "outputs": [],
- "source": [
- "# target_dir = './Data/HR-1/'\n",
- "# filenames = natsort.natsorted([filename for filename in os.listdir(target_dir) if not filename.startswith('.')])\n",
- "# im_list=[load_im(target_dir, file_name) for file_name in tqdm(filenames)][:193]"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 3,
- "id": "52daadf5-4239-4959-bff0-e3826a35a1bb",
- "metadata": {},
- "outputs": [],
- "source": [
- "# np.save('./Data/image_sequence.npy', im_list)"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 4,
"id": "79d2f77c-3fde-4ea7-8b86-8305c2a2ab9c",
"metadata": {},
"outputs": [],
@@ -51,258 +28,74 @@
"im_list = np.load('./data/image_sequence.npy')"
]
},
- {
- "cell_type": "markdown",
- "id": "68a9c407-d577-4c04-b808-8182518ad7f3",
- "metadata": {},
- "source": [
- "### Perform the watershed segmentation to analyze the cell wall defomration"
- ]
- },
{
"cell_type": "code",
- "execution_count": 5,
- "id": "f0a7075d-ec12-40ad-985c-28192f52d146",
+ "execution_count": 3,
+ "id": "02bcfe2f-3b45-4b7b-a227-f79029080531",
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
- "100%|███████████████████████████████████████████| 193/193 [05:36<00:00, 1.74s/it]\n"
+ "100%|█████████████████████████████████████████| 193/193 [05:08<00:00, 1.60s/it]\n"
]
- },
- {
- "data": {
- "text/plain": [
- "0"
- ]
- },
- "execution_count": 5,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "nuclei_list=[] #segemented images\n",
- "centroids_x_list=[] # x axis of centroids\n",
- "centroids_y_list=[] # y axis of centroids\n",
- "frame_num_list=[] # number of frame\n",
- "labels_list=[] # number of labels\n",
- "\n",
- "for i in tqdm(range(len(im_list))):\n",
- " #watershed segmentation\n",
- " nuclei, _=watershed_segmentation(im_list[i])\n",
- " \n",
- " #centroids extraction\n",
- " centroids_y, centroids_x, labels=extract_centroids(nuclei)\n",
- " \n",
- " #frame number\n",
- " frame_num=np.ones(len(centroids_y), dtype=\"int32\")*i\n",
- " \n",
- " #save results\n",
- " nuclei_list.append(nuclei)\n",
- " centroids_y_list.extend(centroids_y)\n",
- " centroids_x_list.extend(centroids_x)\n",
- " frame_num_list.extend(frame_num)\n",
- " labels_list.extend(labels)\n",
- "\n",
- "nuclei_list=np.asarray(nuclei_list)\n",
- "centroids_y_list=np.asarray(centroids_y_list)\n",
- "centroids_x_list=np.asarray(centroids_x_list)\n",
- "frame_num_list=np.asarray(frame_num_list)\n",
- "labels_list=np.asarray(labels_list)\n",
- "\n",
- "#delete im_list and release memory\n",
- "del im_list\n",
- "gc.collect()"
- ]
- },
- {
- "cell_type": "markdown",
- "id": "187a161f-e493-4712-9436-3bed65a72092",
- "metadata": {},
- "source": [
- "### Make Pandas dataframe for individual cell tracking"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 6,
- "id": "6fada159-2c82-4d73-b245-47b812dacbf1",
- "metadata": {},
- "outputs": [
- {
- "data": {
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