Simple threshold mask

088c9931 · fima · 0aa4ce89 · 088c9931
Commit 088c9931 authored 1 year ago by fima
--- a/segmentation/mask_from_filtering_and_threshold.ipynb
+++ b/segmentation/mask_from_filtering_and_threshold.ipynb
@@ -2,7 +2,7 @@
 "cells": [
  {
   "cell_type": "markdown",
-   "id": "0f62fd3b",
+   "id": "cc248896",
   "metadata": {},
   "source": [
    "# Simple 3D binary mask\n",
@@ -12,7 +12,7 @@
  {
   "cell_type": "code",
   "execution_count": 1,
-   "id": "0a23b431",
+   "id": "871f793a",
   "metadata": {},
   "outputs": [],
   "source": [
@@ -25,7 +25,7 @@
  },
  {
   "cell_type": "markdown",
-   "id": "f9ad6ad1",
+   "id": "1854d8dd",
   "metadata": {},
   "source": [
    "## Helper functions"
@@ -34,7 +34,7 @@
  {
   "cell_type": "code",
   "execution_count": 2,
-   "id": "7a3aa8a7",
+   "id": "56ccd2a9",
   "metadata": {},
   "outputs": [],
   "source": [
@@ -63,7 +63,7 @@
  },
  {
   "cell_type": "markdown",
-   "id": "7baf5d58",
+   "id": "107f92f4",
   "metadata": {},
   "source": [
    "## Load data"
@@ -72,7 +72,7 @@
  {
   "cell_type": "code",
   "execution_count": 3,
-   "id": "1f5d1fb6",
+   "id": "a9b977b3",
   "metadata": {},
   "outputs": [
    {
@@ -105,7 +105,7 @@
  },
  {
   "cell_type": "markdown",
-   "id": "66d5bcc7",
+   "id": "186f46cc",
   "metadata": {},
   "source": [
    "## Apply median filter"
@@ -114,7 +114,7 @@
  {
   "cell_type": "code",
   "execution_count": 4,
-   "id": "47b7de23",
+   "id": "1b1fcba9",
   "metadata": {},
   "outputs": [
    {
@@ -147,7 +147,7 @@
  },
  {
   "cell_type": "markdown",
-   "id": "06e9af21",
+   "id": "c17d275c",
   "metadata": {},
   "source": [
    "## Get the threshold value"
@@ -156,7 +156,7 @@
  {
   "cell_type": "code",
   "execution_count": 5,
-   "id": "06bba77b",
+   "id": "aebf7d46",
   "metadata": {},
   "outputs": [
    {
@@ -186,7 +186,7 @@
  },
  {
   "cell_type": "markdown",
-   "id": "b2dc8937",
+   "id": "c6e49b28",
   "metadata": {},
   "source": [
    "## Make binary mask"
@@ -195,7 +195,7 @@
  {
   "cell_type": "code",
   "execution_count": 6,
-   "id": "9971ddcb",
+   "id": "ec9a9333",
   "metadata": {},
   "outputs": [
    {

-%% Cell type:markdown id:0f62fd3b tags:
+%% Cell type:markdown id:cc248896 tags:
  
 # Simple 3D binary mask
 author: Felipe Delestro (fima@dtu.dk)
  
-%% Cell type:code id:0a23b431 tags:
+%% Cell type:code id:871f793a tags:
  
 ``` python
 import qim3d
 import numpy as np
 import scipy.ndimage
 import matplotlib.pyplot as plt
 from skimage import filters
 ```
  
-%% Cell type:markdown id:f9ad6ad1 tags:
+%% Cell type:markdown id:1854d8dd tags:
  
 ## Helper functions
  
-%% Cell type:code id:7a3aa8a7 tags:
+%% Cell type:code id:56ccd2a9 tags:
  
 ``` python
 def viz(vol, cmap="viridis"):
    qim3d.viz.slice_viz(vol, position=np.linspace(50,100, num=6).astype(int), img_height=4, cmap=cmap)
  
 def histogram(vol, vline=None):
  
    # Calculate histogram
    vol_hist, bin_edges = np.histogram(vol, bins=16)
  
    # Plot histogram
    fig, ax = plt.subplots(figsize=(6, 4))
    ax.bar(bin_edges[:-1], vol_hist, width=np.diff(bin_edges), ec="white", align="edge")
  
    if vline:
        ax.axvline(vline, color="#FF3366", linestyle="--")
  
    # Adjustments
    ax.spines["right"].set_visible(False)
    ax.spines["top"].set_visible(False)
    ax.set_yscale("log")
  
    plt.show()
 ```
  
-%% Cell type:markdown id:7baf5d58 tags:
+%% Cell type:markdown id:107f92f4 tags:
  
 ## Load data
  
-%% Cell type:code id:1f5d1fb6 tags:
+%% Cell type:code id:a9b977b3 tags:
  
 ``` python
 # Load data
 vol = qim3d.io.load("../resources/img3d/shell_225x128x128.tif")
 viz(vol)
 histogram(vol)
 ```
  
 %% Output
  

  

  
-%% Cell type:markdown id:66d5bcc7 tags:
+%% Cell type:markdown id:186f46cc tags:
  
 ## Apply median filter
  
-%% Cell type:code id:47b7de23 tags:
+%% Cell type:code id:1b1fcba9 tags:
  
 ``` python
 # Median filter
 vol = scipy.ndimage.median_filter(vol, size=3)
 viz(vol)
 histogram(vol)
 ```
  
 %% Output
  

  

  
-%% Cell type:markdown id:06e9af21 tags:
+%% Cell type:markdown id:c17d275c tags:
  
 ## Get the threshold value
  
-%% Cell type:code id:06bba77b tags:
+%% Cell type:code id:aebf7d46 tags:
  
 ``` python
 # Get the Otsu thresold
 thresh = filters.threshold_otsu(vol)
 print (f"Threshold value: {thresh}")
 histogram(vol, vline=thresh)
 ```
  
 %% Output
  
    Threshold value: 63
  

  
-%% Cell type:markdown id:b2dc8937 tags:
+%% Cell type:markdown id:c6e49b28 tags:
  
 ## Make binary mask
  
-%% Cell type:code id:9971ddcb tags:
+%% Cell type:code id:ec9a9333 tags:
  
 ``` python
 # Make it binary
 vol = vol > thresh
 viz(vol, cmap="gray")
 ```
  
 %% Output