deploy: phasorpy/phasorpy@1df6fb9

main/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 6a1d0a9c1312d1a5df376d628fa2dfc5
+config: 8b702b1bb427bbb58c36af3bd5837df4
 tags: 645f666f9bcd5a90fca523b33c5a78b7

main/_downloads/19192f653cbb57a934e348239ca7e840/phasorpy_cursors.ipynb

@@ -0,0 +1,165 @@
+{
+  "cells": [
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "\n# Cursors\n\nAn introduction to selecting phasor coordinates using cursors.\n"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "Import required modules, functions, and classes:\n\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "import matplotlib.pyplot as plt\nimport tifffile\n\nfrom phasorpy.color import CATEGORICAL\nfrom phasorpy.cursors import (\n    mask_from_circular_cursor,\n    mask_from_polar_cursor,\n    pseudo_color,\n)\nfrom phasorpy.datasets import fetch\nfrom phasorpy.phasor import phasor_from_signal, phasor_to_polar\nfrom phasorpy.plot import PhasorPlot"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "## Circular cursors\n\nUse circular cursors in the phasor space to mask regions of interest:\n\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "signal = tifffile.imread(fetch('paramecium.lsm'))\nmean, real, imag = phasor_from_signal(signal, axis=0)\ncursors_real = [-0.33, 0.55]\ncursors_imag = [-0.72, -0.72]\ncircular_mask = mask_from_circular_cursor(\n    real, imag, cursors_real, cursors_imag, radius=0.2\n)"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "Show the circular cursors in the phasor plot:\n\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "threshold = mean > 1\n\nplot = PhasorPlot(allquadrants=True, title='Two circular cursors')\nplot.hist2d(real[threshold], imag[threshold])\nfor i in range(len(cursors_real)):\n    plot.cursor(\n        cursors_real[i],\n        cursors_imag[i],\n        radius=0.2,\n        color=CATEGORICAL[i],\n        linestyle='-',\n    )"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "## Polar cursor\n\nCreate a mask with phase and modulation values:\n\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "phase, mod = phasor_to_polar(real, imag)\n\nphase_range = [[-2.27, -1.57], [-1.22, -0.70]]\nmodulation_range = [[0.7, 0.9], [0.8, 1.0]]\npolar_mask = mask_from_polar_cursor(phase, mod, phase_range, modulation_range)"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "Show cursors in the phasor plot:\n\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "plot = PhasorPlot(allquadrants=True, title='Two polar cursors')\nplot.hist2d(real[threshold], imag[threshold], cmap='Blues')\nfor i in range(len(phase_range[0])):\n    plot.polar_cursor(\n        phase=phase_range[i][0],\n        phase_limit=phase_range[i][1],\n        modulation=modulation_range[i][0],\n        modulation_limit=modulation_range[i][1],\n        color=CATEGORICAL[i + 2],\n        linestyle='-',\n    )"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "## Pseudo-color\n\nAverage images can be pseudo-colored (segmented) using cursor's masks.\nSegmented image with circular cursors:\n\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "segmented_image = pseudo_color(mean, circular_mask)\n\nfig, ax = plt.subplots()\nax.set_title('Segmented image with circular cursors')\nax.imshow(segmented_image)\nplt.show()"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "Segmented image with polar cursors:\n\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "segmented_image = pseudo_color(mean, polar_mask, colors=CATEGORICAL[2:])\n\nfig, ax = plt.subplots()\nax.set_title('Segmented image with polar cursors')\nax.imshow(segmented_image)\nplt.show()"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "sphinx_gallery_thumbnail_number = 1\n\n"
+      ]
+    }
+  ],
+  "metadata": {
+    "kernelspec": {
+      "display_name": "Python 3",
+      "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": "3.11.9"
+    }
+  },
+  "nbformat": 4,
+  "nbformat_minor": 0
+}

main/_downloads/78c7466b0ab259d8505a9a93cf280ce0/phasorpy_cursors.py

@@ -0,0 +1,107 @@
+"""
+Cursors
+=======
+
+An introduction to selecting phasor coordinates using cursors.
+
+"""
+
+# %%
+# Import required modules, functions, and classes:
+
+import matplotlib.pyplot as plt
+import tifffile
+
+from phasorpy.color import CATEGORICAL
+from phasorpy.cursors import (
+    mask_from_circular_cursor,
+    mask_from_polar_cursor,
+    pseudo_color,
+)
+from phasorpy.datasets import fetch
+from phasorpy.phasor import phasor_from_signal, phasor_to_polar
+from phasorpy.plot import PhasorPlot
+
+# %%
+# Circular cursors
+# ----------------
+#
+# Use circular cursors in the phasor space to mask regions of interest:
+
+signal = tifffile.imread(fetch('paramecium.lsm'))
+mean, real, imag = phasor_from_signal(signal, axis=0)
+cursors_real = [-0.33, 0.55]
+cursors_imag = [-0.72, -0.72]
+circular_mask = mask_from_circular_cursor(
+    real, imag, cursors_real, cursors_imag, radius=0.2
+)
+
+# %%
+# Show the circular cursors in the phasor plot:
+
+threshold = mean > 1
+
+plot = PhasorPlot(allquadrants=True, title='Two circular cursors')
+plot.hist2d(real[threshold], imag[threshold])
+for i in range(len(cursors_real)):
+    plot.cursor(
+        cursors_real[i],
+        cursors_imag[i],
+        radius=0.2,
+        color=CATEGORICAL[i],
+        linestyle='-',
+    )
+
+# %%
+# Polar cursor
+# ------------
+#
+# Create a mask with phase and modulation values:
+
+phase, mod = phasor_to_polar(real, imag)
+
+phase_range = [[-2.27, -1.57], [-1.22, -0.70]]
+modulation_range = [[0.7, 0.9], [0.8, 1.0]]
+polar_mask = mask_from_polar_cursor(phase, mod, phase_range, modulation_range)
+
+# %%
+# Show cursors in the phasor plot:
+
+plot = PhasorPlot(allquadrants=True, title='Two polar cursors')
+plot.hist2d(real[threshold], imag[threshold], cmap='Blues')
+for i in range(len(phase_range[0])):
+    plot.polar_cursor(
+        phase=phase_range[i][0],
+        phase_limit=phase_range[i][1],
+        modulation=modulation_range[i][0],
+        modulation_limit=modulation_range[i][1],
+        color=CATEGORICAL[i + 2],
+        linestyle='-',
+    )
+
+# %%
+# Pseudo-color
+# ------------
+#
+# Average images can be pseudo-colored (segmented) using cursor's masks.
+# Segmented image with circular cursors:
+
+segmented_image = pseudo_color(mean, circular_mask)
+
+fig, ax = plt.subplots()
+ax.set_title('Segmented image with circular cursors')
+ax.imshow(segmented_image)
+plt.show()
+
+# %%
+# Segmented image with polar cursors:
+
+segmented_image = pseudo_color(mean, polar_mask, colors=CATEGORICAL[2:])
+
+fig, ax = plt.subplots()
+ax.set_title('Segmented image with polar cursors')
+ax.imshow(segmented_image)
+plt.show()
+
+# %%
+# sphinx_gallery_thumbnail_number = 1

main/_modules/index.html

@@ -456,6 +456,7 @@
   <h1>All modules for which code is available</h1>
 <ul><li><a href="phasorpy/color.html">phasorpy.color</a></li>
 <li><a href="phasorpy/components.html">phasorpy.components</a></li>
+<li><a href="phasorpy/cursors.html">phasorpy.cursors</a></li>
 <li><a href="phasorpy/datasets.html">phasorpy.datasets</a></li>
 <li><a href="phasorpy/io.html">phasorpy.io</a></li>
 <li><a href="phasorpy/phasor.html">phasorpy.phasor</a></li>
@@ -512,7 +513,7 @@ <h1>All modules for which code is available</h1>
         <div class="footer-item">
 
   <p class="sphinx-version">
-    Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.3.7.
+    Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.4.5.
     <br/>
   </p>
 </div>

main/_modules/phasorpy/color.html

@@ -1094,7 +1094,7 @@ <h1>Source code for phasorpy.color</h1><div class="highlight"><pre>
         <div class="footer-item">
 
   <p class="sphinx-version">
-    Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.3.7.
+    Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.4.5.
     <br/>
   </p>
 </div>

main/_modules/phasorpy/components.html

@@ -765,7 +765,7 @@ <h1>Source code for phasorpy.components</h1><div class="highlight"><pre>
         <div class="footer-item">
 
   <p class="sphinx-version">
-    Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.3.7.
+    Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.4.5.
     <br/>
   </p>
 </div>