JNB: Iterate over all contours, not just first contour

rochefort-lab · Jul 11, 2021 · 6fe91cb · 6fe91cb
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Showing 4 changed files with 56 additions and 48 deletions.
diff --git a/examples/Basic usage.ipynb b/examples/Basic usage.ipynb
@@ -246,23 +246,25 @@
     "\n",
     "# Plot all the neuropil regions in yellow\n",
     "for i_npil in range(1, n_npil + 1):\n",
+    "    for contour in experiment.roi_polys[roi, trial][i_npil]:\n",
+    "        plt.fill(\n",
+    "            contour[:, 1],\n",
+    "            contour[:, 0],\n",
+    "            facecolor=\"none\",\n",
+    "            edgecolor=\"y\",\n",
+    "            alpha=0.6,\n",
+    "        )\n",
+    "\n",
+    "# Plot the ROI outline in red\n",
+    "for contour in experiment.roi_polys[roi, trial][0]:\n",
     "    plt.fill(\n",
-    "        experiment.roi_polys[roi, trial][i_npil][0][:, 1],\n",
-    "        experiment.roi_polys[roi, trial][i_npil][0][:, 0],\n",
+    "        contour[:, 1],\n",
+    "        contour[:, 0],\n",
     "        facecolor=\"none\",\n",
-    "        edgecolor=\"y\",\n",
+    "        edgecolor=\"r\",\n",
     "        alpha=0.6,\n",
     "    )\n",
     "\n",
-    "# Plot the ROI outline in red\n",
-    "plt.fill(\n",
-    "    experiment.roi_polys[roi, trial][0][0][:, 1],\n",
-    "    experiment.roi_polys[roi, trial][0][0][:, 0],\n",
-    "    facecolor=\"none\",\n",
-    "    edgecolor=\"r\",\n",
-    "    alpha=0.6,\n",
-    ")\n",
-    "\n",
     "# Reset axes limits\n",
     "plt.xlim(XLIM)\n",
     "plt.ylim(YLIM)\n",
@@ -284,12 +286,13 @@
     "plt.imshow(experiment.means[trial], cmap=\"gray\")\n",
     "\n",
     "# Plot each of the cells\n",
-    "for roi_poly in experiment.roi_polys:\n",
-    "    plt.fill(\n",
-    "        roi_poly[trial][0][0][:, 1],\n",
-    "        roi_poly[trial][0][0][:, 0],\n",
-    "        alpha=0.3,\n",
-    "    )\n",
+    "for i_roi in range(len(experiment.roi_polys)):\n",
+    "    for contour in experiment.roi_polys[i_roi, trial][0]:\n",
+    "        plt.fill(\n",
+    "            contour[:, 1],\n",
+    "            contour[:, 0],\n",
+    "            alpha=0.3,\n",
+    "        )\n",
     "\n",
     "plt.show()"
    ]
@@ -669,23 +672,25 @@
     "\n",
     "# Plot all the neuropil regions in yellow\n",
     "for i_npil in range(1, n_npil + 1):\n",
+    "    for contour in experiment.roi_polys[roi, trial][i_npil]:\n",
+    "        plt.fill(\n",
+    "            contour[:, 1],\n",
+    "            contour[:, 0],\n",
+    "            facecolor=\"none\",\n",
+    "            edgecolor=\"y\",\n",
+    "            alpha=0.6,\n",
+    "        )\n",
+    "\n",
+    "# Plot the ROI outline in red\n",
+    "for contour in experiment.roi_polys[roi, trial][0]:\n",
     "    plt.fill(\n",
-    "        experiment.roi_polys[roi, trial][i_npil][0][:, 1],\n",
-    "        experiment.roi_polys[roi, trial][i_npil][0][:, 0],\n",
+    "        contour[:, 1],\n",
+    "        contour[:, 0],\n",
     "        facecolor=\"none\",\n",
-    "        edgecolor=\"y\",\n",
+    "        edgecolor=\"r\",\n",
     "        alpha=0.6,\n",
     "    )\n",
     "\n",
-    "# Plot the ROI outline in red\n",
-    "plt.fill(\n",
-    "    experiment.roi_polys[roi, trial][0][0][:, 1],\n",
-    "    experiment.roi_polys[roi, trial][0][0][:, 0],\n",
-    "    facecolor=\"none\",\n",
-    "    edgecolor=\"r\",\n",
-    "    alpha=0.6,\n",
-    ")\n",
-    "\n",
     "# Reset axes limits\n",
     "plt.xlim(XLIM)\n",
     "plt.ylim(YLIM)\n",

diff --git a/examples/SIMA example.ipynb b/examples/SIMA example.ipynb
@@ -212,13 +212,14 @@
     "# Plot the mean image and ROIs from the FISSA experiment\n",
     "plt.imshow(experiment.means[trial], cmap=\"gray\")\n",
     "\n",
-    "for i_roi, roi_poly in enumerate(experiment.roi_polys):\n",
+    "for i_roi in range(len(experiment.roi_polys)):\n",
     "    # Plot border around ROI\n",
-    "    plt.plot(\n",
-    "        roi_poly[trial][0][0][:, 1],\n",
-    "        roi_poly[trial][0][0][:, 0],\n",
-    "        color=cmap((i_roi * 2 + 1) % cmap.N),\n",
-    "    )\n",
+    "    for contour in experiment.roi_polys[i_roi, trial][0]:\n",
+    "        plt.plot(\n",
+    "            contour[:, 1],\n",
+    "            contour[:, 0],\n",
+    "            color=cmap((i_roi * 2 + 1) % cmap.N),\n",
+    "        )\n",
     "\n",
     "plt.show()"
    ]

diff --git a/examples/Suite2p example.ipynb b/examples/Suite2p example.ipynb
@@ -171,13 +171,14 @@
     "XLIM = plt.xlim()\n",
     "YLIM = plt.ylim()\n",
     "\n",
-    "for i_roi, roi_poly in enumerate(experiment.roi_polys):\n",
+    "for i_roi in range(len(experiment.roi_polys)):\n",
     "    # Plot border around ROI\n",
-    "    plt.plot(\n",
-    "        roi_poly[trial][0][0][:, 1],\n",
-    "        roi_poly[trial][0][0][:, 0],\n",
-    "        color=cmap((i_roi * 2 + 1) % cmap.N),\n",
-    "    )\n",
+    "    for contour in experiment.roi_polys[i_roi, trial][0]:\n",
+    "        plt.plot(\n",
+    "            contour[:, 1],\n",
+    "            contour[:, 0],\n",
+    "            color=cmap((i_roi * 2 + 1) % cmap.N),\n",
+    "        )\n",
     "\n",
     "# ROI co-ordinates are half a pixel outside the image,\n",
     "# so we reset the axis limits\n",

diff --git a/examples/cNMF example.ipynb b/examples/cNMF example.ipynb
@@ -191,13 +191,14 @@
     "XLIM = plt.xlim()\n",
     "YLIM = plt.ylim()\n",
     "\n",
-    "for i_roi, roi_poly in enumerate(experiment.roi_polys):\n",
+    "for i_roi in range(len(experiment.roi_polys)):\n",
     "    # Plot border around ROI\n",
-    "    plt.plot(\n",
-    "        roi_poly[trial][0][0][:, 1],\n",
-    "        roi_poly[trial][0][0][:, 0],\n",
-    "        color=cmap((i_roi * 2 + 1) % cmap.N),\n",
-    "    )\n",
+    "    for contour in experiment.roi_polys[i_roi, trial][0]:\n",
+    "        plt.plot(\n",
+    "            contour[:, 1],\n",
+    "            contour[:, 0],\n",
+    "            color=cmap((i_roi * 2 + 1) % cmap.N),\n",
+    "        )\n",
     "\n",
     "# ROI co-ordinates are half a pixel outside the image,\n",
     "# so we reset the axis limits\n",