tidy up

bmandracchia · Sep 3, 2024 · 184764b · 184764b
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diff --git a/_proc/00_core.ipynb b/_proc/00_core.ipynb
@@ -44,7 +44,7 @@
       "text/markdown": [
        "---\n",
        "\n",
-       "[source](https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/core.py#L26){target=\"_blank\" style=\"float:right; font-size:smaller\"}\n",
+       "[source](https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/core.py#L29){target=\"_blank\" style=\"float:right; font-size:smaller\"}\n",
        "\n",
        "### attributesFromDict\n",
        "\n",
@@ -53,7 +53,7 @@
       "text/plain": [
        "---\n",
        "\n",
-       "[source](https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/core.py#L26){target=\"_blank\" style=\"float:right; font-size:smaller\"}\n",
+       "[source](https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/core.py#L29){target=\"_blank\" style=\"float:right; font-size:smaller\"}\n",
        "\n",
        "### attributesFromDict\n",
        "\n",
@@ -71,6 +71,80 @@
     "show_doc(attributesFromDict)"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/markdown": [
+       "---\n",
+       "\n",
+       "[source](https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/core.py#L35){target=\"_blank\" style=\"float:right; font-size:smaller\"}\n",
+       "\n",
+       "### img2float\n",
+       "\n",
+       ">      img2float (image, force_copy=False)"
+      ],
+      "text/plain": [
+       "---\n",
+       "\n",
+       "[source](https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/core.py#L35){target=\"_blank\" style=\"float:right; font-size:smaller\"}\n",
+       "\n",
+       "### img2float\n",
+       "\n",
+       ">      img2float (image, force_copy=False)"
+      ]
+     },
+     "execution_count": 2,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "#| echo: false\n",
+    "#| output: asis\n",
+    "show_doc(img2float)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/markdown": [
+       "---\n",
+       "\n",
+       "[source](https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/core.py#L39){target=\"_blank\" style=\"float:right; font-size:smaller\"}\n",
+       "\n",
+       "### img2Tensor\n",
+       "\n",
+       ">      img2Tensor (image)"
+      ],
+      "text/plain": [
+       "---\n",
+       "\n",
+       "[source](https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/core.py#L39){target=\"_blank\" style=\"float:right; font-size:smaller\"}\n",
+       "\n",
+       "### img2Tensor\n",
+       "\n",
+       ">      img2Tensor (image)"
+      ]
+     },
+     "execution_count": 3,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "#| echo: false\n",
+    "#| output: asis\n",
+    "show_doc(img2Tensor)"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},

diff --git a/_proc/04_nets.ipynb b/_proc/04_nets.ipynb
@@ -1199,10 +1199,6 @@
    "language": "python",
    "name": "python3"
   },
-  "language_info": {
-   "name": "python",
-   "version": "3.11.5"
-  },
   "widgets": {
    "application/vnd.jupyter.widget-state+json": {
     "state": {},

diff --git a/_proc/06_metrics.ipynb b/_proc/06_metrics.ipynb
@@ -30,13 +30,17 @@
       "text/markdown": [
        "---\n",
        "\n",
+       "[source](https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/metrics.py#L20){target=\"_blank\" style=\"float:right; font-size:smaller\"}\n",
+       "\n",
        "### SSIMMetric\n",
        "\n",
        ">      SSIMMetric (x, y, spatial_dims=2)"
       ],
       "text/plain": [
        "---\n",
        "\n",
+       "[source](https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/metrics.py#L20){target=\"_blank\" style=\"float:right; font-size:smaller\"}\n",
+       "\n",
        "### SSIMMetric\n",
        "\n",
        ">      SSIMMetric (x, y, spatial_dims=2)"

diff --git a/_proc/09_visualize.ipynb b/_proc/09_visualize.ipynb
@@ -29,7 +29,7 @@
    "outputs": [],
    "source": [
     "# load sample data\n",
-    "data4D = util.img_as_float(cells3d())\n",
+    "data4D = img2float(cells3d())\n",
     "data = data4D[:, 1, :, :] # load the nuclei channel"
    ]
   },
@@ -52,7 +52,7 @@
       "text/markdown": [
        "---\n",
        "\n",
-       "[source](https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/visualize.py#L23){target=\"_blank\" style=\"float:right; font-size:smaller\"}\n",
+       "[source](https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/visualize.py#L22){target=\"_blank\" style=\"float:right; font-size:smaller\"}\n",
        "\n",
        "### plot_image\n",
        "\n",
@@ -69,7 +69,7 @@
       "text/plain": [
        "---\n",
        "\n",
-       "[source](https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/visualize.py#L23){target=\"_blank\" style=\"float:right; font-size:smaller\"}\n",
+       "[source](https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/visualize.py#L22){target=\"_blank\" style=\"float:right; font-size:smaller\"}\n",
        "\n",
        "### plot_image\n",
        "\n",
@@ -126,7 +126,7 @@
       "text/markdown": [
        "---\n",
        "\n",
-       "[source](https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/visualize.py#L57){target=\"_blank\" style=\"float:right; font-size:smaller\"}\n",
+       "[source](https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/visualize.py#L56){target=\"_blank\" style=\"float:right; font-size:smaller\"}\n",
        "\n",
        "### mosaic_image_3d\n",
        "\n",
@@ -147,7 +147,7 @@
       "text/plain": [
        "---\n",
        "\n",
-       "[source](https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/visualize.py#L57){target=\"_blank\" style=\"float:right; font-size:smaller\"}\n",
+       "[source](https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/visualize.py#L56){target=\"_blank\" style=\"float:right; font-size:smaller\"}\n",
        "\n",
        "### mosaic_image_3d\n",
        "\n",
@@ -187,7 +187,7 @@
       "text/markdown": [
        "---\n",
        "\n",
-       "[source](https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/visualize.py#L112){target=\"_blank\" style=\"float:right; font-size:smaller\"}\n",
+       "[source](https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/visualize.py#L111){target=\"_blank\" style=\"float:right; font-size:smaller\"}\n",
        "\n",
        "### show_images_grid\n",
        "\n",
@@ -216,7 +216,7 @@
       "text/plain": [
        "---\n",
        "\n",
-       "[source](https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/visualize.py#L112){target=\"_blank\" style=\"float:right; font-size:smaller\"}\n",
+       "[source](https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/visualize.py#L111){target=\"_blank\" style=\"float:right; font-size:smaller\"}\n",
        "\n",
        "### show_images_grid\n",
        "\n",
@@ -315,7 +315,7 @@
       "text/markdown": [
        "---\n",
        "\n",
-       "[source](https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/visualize.py#L184){target=\"_blank\" style=\"float:right; font-size:smaller\"}\n",
+       "[source](https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/visualize.py#L183){target=\"_blank\" style=\"float:right; font-size:smaller\"}\n",
        "\n",
        "### show_plane\n",
        "\n",
@@ -334,7 +334,7 @@
       "text/plain": [
        "---\n",
        "\n",
-       "[source](https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/visualize.py#L184){target=\"_blank\" style=\"float:right; font-size:smaller\"}\n",
+       "[source](https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/visualize.py#L183){target=\"_blank\" style=\"float:right; font-size:smaller\"}\n",
        "\n",
        "### show_plane\n",
        "\n",
@@ -372,7 +372,7 @@
       "text/markdown": [
        "---\n",
        "\n",
-       "[source](https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/visualize.py#L208){target=\"_blank\" style=\"float:right; font-size:smaller\"}\n",
+       "[source](https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/visualize.py#L207){target=\"_blank\" style=\"float:right; font-size:smaller\"}\n",
        "\n",
        "### visualize_slices\n",
        "\n",
@@ -387,7 +387,7 @@
       "text/plain": [
        "---\n",
        "\n",
-       "[source](https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/visualize.py#L208){target=\"_blank\" style=\"float:right; font-size:smaller\"}\n",
+       "[source](https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/visualize.py#L207){target=\"_blank\" style=\"float:right; font-size:smaller\"}\n",
        "\n",
        "### visualize_slices\n",
        "\n",
@@ -465,7 +465,7 @@
       "text/markdown": [
        "---\n",
        "\n",
-       "[source](https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/visualize.py#L243){target=\"_blank\" style=\"float:right; font-size:smaller\"}\n",
+       "[source](https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/visualize.py#L242){target=\"_blank\" style=\"float:right; font-size:smaller\"}\n",
        "\n",
        "### slice_explorer\n",
        "\n",
@@ -482,7 +482,7 @@
       "text/plain": [
        "---\n",
        "\n",
-       "[source](https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/visualize.py#L243){target=\"_blank\" style=\"float:right; font-size:smaller\"}\n",
+       "[source](https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/visualize.py#L242){target=\"_blank\" style=\"float:right; font-size:smaller\"}\n",
        "\n",
        "### slice_explorer\n",
        "\n",
@@ -7457,7 +7457,7 @@
       "text/markdown": [
        "---\n",
        "\n",
-       "[source](https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/visualize.py#L273){target=\"_blank\" style=\"float:right; font-size:smaller\"}\n",
+       "[source](https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/visualize.py#L272){target=\"_blank\" style=\"float:right; font-size:smaller\"}\n",
        "\n",
        "### plot_volume\n",
        "\n",
@@ -7481,7 +7481,7 @@
       "text/plain": [
        "---\n",
        "\n",
-       "[source](https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/visualize.py#L273){target=\"_blank\" style=\"float:right; font-size:smaller\"}\n",
+       "[source](https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/visualize.py#L272){target=\"_blank\" style=\"float:right; font-size:smaller\"}\n",
        "\n",
        "### plot_volume\n",
        "\n",

diff --git a/bioMONAI/_modidx.py b/bioMONAI/_modidx.py
@@ -94,7 +94,8 @@
                                'bioMONAI.nets.get_padding': ('nets.html#get_padding', 'bioMONAI/nets.py'),
                                'bioMONAI.nets.interpolate': ('nets.html#interpolate', 'bioMONAI/nets.py')},
             'bioMONAI.template': {'bioMONAI.template.foo': ('template.html#foo', 'bioMONAI/template.py')},
-            'bioMONAI.transforms': { 'bioMONAI.transforms.RandCrop2D': ('transforms.html#randcrop2d', 'bioMONAI/transforms.py'),
+            'bioMONAI.transforms': { 'bioMONAI.transforms.RandCameraNoise': ('transforms.html#randcameranoise', 'bioMONAI/transforms.py'),
+                                     'bioMONAI.transforms.RandCrop2D': ('transforms.html#randcrop2d', 'bioMONAI/transforms.py'),
                                      'bioMONAI.transforms.RandCrop2D.__init__': ( 'transforms.html#randcrop2d.__init__',
                                                                                   'bioMONAI/transforms.py'),
                                      'bioMONAI.transforms.RandCrop2D.before_call': ( 'transforms.html#randcrop2d.before_call',