Merge pull request #17 from fercer/dev-content

Updated gpu instructions to consider mps

Author: fercer

notebooks/Solved_Zarr_and_Dask_for_large-scale_imaging-Part-2.ipynb

@@ -80,14 +80,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 3,
    "metadata": {
     "executionInfo": {
      "elapsed": 976,
@@ -120,11 +113,11 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 8,
    "metadata": {},
    "outputs": [],
    "source": [
-    "# input_path = /path/to/local/image\n",
+    "# input_path = \"CMU-1_Crop.ome.zarr\"\n",
     "input_path = \"https://storage.googleapis.com/jax-public-ngff/example_v2/CMU-1_Crop.ome.zarr\""
    ]
   },
@@ -152,7 +145,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 20,
    "metadata": {
     "cellView": "form",
     "colab": {
@@ -176,7 +169,7 @@
     "from cellpose import models, transforms\n",
     "import torch\n",
     "\n",
-    "gpu = torch.cuda.is_available()\n",
+    "gpu = torch.cuda.is_available() or torch.mps.is_available()\n",
     "model_type = \"cyto3\"\n",
     "\n",
     "cellpose_model = models.CellposeModel(gpu=gpu, model_type=model_type)"
@@ -202,24 +195,7 @@
    "execution_count": null,
    "metadata": {},
    "outputs": [],
-   "source": [
-    "img_t = transforms.convert_image(da_sel.compute(), channel_axis=2, channels=[0, 0])\n",
-    "img_t = transforms.normalize_img(img_t, invert=False, axis=2)\n",
-    "\n",
-    "labels, _, _ = cellpose_model.eval(img_t[None, ...], diameter=None, flow_threshold=None, channels=[0, 0])"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "id": "iRTdgTzi_KfU"
-   },
-   "outputs": [],
-   "source": [
-    "plt.imshow(da_sel)\n",
-    "plt.imshow(skimage.color.label2rgb(labels), alpha=0.5)"
-   ]
+   "source": []
   },
   {
    "cell_type": "markdown",
@@ -321,7 +297,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 41,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -449,7 +425,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 66,
    "metadata": {
     "id": "2yzM2YNRcAFI"
    },
@@ -515,39 +491,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "cellView": "form",
-    "id": "Bh6c9EVy9hST"
-   },
-   "outputs": [],
-   "source": [
-    "with ProgressBar():\n",
-    "    for s in range(1, 6):\n",
-    "        da_labels = da.from_zarr(\"CMU-1_Crop_labels_cellpose_cyto3.zarr\", component=str(s - 1))\n",
-    "\n",
-    "        da_labels_ds = da_labels[::2, ::2]\n",
-    "        da_labels_ds = da_labels_ds.rechunk()\n",
-    "\n",
-    "        da_labels_ds.to_zarr(\n",
-    "            \"CMU-1_Crop_labels_cellpose_cyto3.zarr\",\n",
-    "            component=str(s),\n",
-    "            write_empty_chunks=False,\n",
-    "            compressor=zarr.Blosc(clevel=9),\n",
-    "            overwrite=True\n",
-    "        )"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "cellView": "form",
-    "id": "Bh6c9EVy9hST"
-   },
+   "metadata": {},
    "outputs": [],
-   "source": [
-    "z_labels = zarr.open(\"CMU-1_Crop_labels_cellpose_cyto3.zarr\", mode=\"a\")"
-   ]
+   "source": []
   },
   {
    "cell_type": "markdown",
@@ -558,7 +504,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 76,
    "metadata": {
     "cellView": "form",
     "id": "Bh6c9EVy9hST"
@@ -585,7 +531,7 @@
     "                \"path\" : str(s),\n",
     "                \"coordinateTransformations\": [\n",
     "                    {\n",
-    "                        \"scale\" : [4.942E-4 / (2**s), 4.942E-4 / (2**s)],\n",
+    "                        \"scale\" : [0.499 / (2**s), 0.499 / (2**s)],\n",
     "                        \"type\" : \"scale\"\n",
     "                    }\n",
     "                ]\n",
@@ -600,13 +546,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "id": "giJcwW_F3vrF"
-   },
+   "metadata": {},
    "outputs": [],
-   "source": [
-    "z_labels = zarr.open(\"CMU-1_Crop_labels_cellpose_cyto3.zarr\", mode=\"r\")"
-   ]
+   "source": []
   },
   {
    "cell_type": "markdown",