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Merge pull request #183 from AnthonyAndroulakis/test_images
Add test_images.ipynb notebook example
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‎examples/test_images.ipynb‎

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{
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"cells": [
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{
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"cell_type": "markdown",
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"id": "2181bf6a-68c4-4869-a1bb-4225b9b7d53f",
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"metadata": {},
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"source": [
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"# Import necessary modules"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "5e21c83d-cb4d-4c5b-a255-4c2834abd93c",
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"metadata": {},
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"outputs": [],
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"source": [
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"import pathlib\n",
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"\n",
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"import ipywidgets as widgets\n",
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"from IPython.display import display\n",
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"\n",
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"import ipyniivue\n",
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"from ipyniivue import NiiVue, download_dataset"
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]
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},
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{
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"cell_type": "markdown",
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"id": "dfc76d81-1331-428a-a64b-5087dbbcf8be",
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"metadata": {},
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"source": [
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"# Download Formats"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "e70f5a26-4a37-4887-a3c0-327818181289",
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"metadata": {},
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"outputs": [],
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"source": [
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"DATA_FOLDER = pathlib.Path(ipyniivue.__file__).parent / \"images\"\n",
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"\n",
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"local_imgs = [\n",
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" \"FLAIR.nrrd\",\n",
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" \"cactus.nii.gz\",\n",
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" \"DoG.png\",\n",
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" \"anat_final.FT+tlrc.HEAD\",\n",
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" \"mha.mha\",\n",
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" \"template.mif.gz\",\n",
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" \"trix/fa.mif\",\n",
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" \"dsistudio.src.gz\",\n",
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" \"dsistudio.fib.gz\",\n",
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" \"wm.mgz\",\n",
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"]\n",
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"\n",
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"files_to_download_local = local_imgs.copy()\n",
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"for img in local_imgs:\n",
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" if img.endswith(\".HEAD\"):\n",
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" # Also need to download the paired .BRIK file\n",
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" brik_file = img.replace(\".HEAD\", \".BRIK\")\n",
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" files_to_download_local.append(brik_file)\n",
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"\n",
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"download_dataset(\n",
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" api_url=\"https://niivue.com/demos/images/\",\n",
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" dest_folder=DATA_FOLDER,\n",
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" files=files_to_download_local,\n",
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")"
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]
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},
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{
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"cell_type": "markdown",
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"id": "af6729b4-2f0e-4a76-b493-eba46cbcdf14",
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"metadata": {},
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"source": [
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"# Download Modalities"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "6e1f8e7f-3eed-40d6-aa8e-828ec08a31ec",
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"metadata": {},
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"outputs": [],
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"source": [
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"modalities_imgs = [\n",
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" \"chris_MRA\",\n",
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" \"chris_PD\",\n",
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" \"chris_t1\",\n",
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" \"chris_t2\",\n",
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" \"CT_Abdo\",\n",
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" \"CT_AVM\",\n",
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" \"CT_Electrodes\",\n",
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" \"CT_Philips\",\n",
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" \"CT_pitch\",\n",
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" \"fmri_pitch\",\n",
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" \"Iguana\",\n",
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" \"mni152\",\n",
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" \"MR_Gd\",\n",
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" \"pcasl\",\n",
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" \"spm152\",\n",
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" \"spmMotor\",\n",
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" \"visiblehuman\",\n",
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" \"rgb_bmp.jpg\",\n",
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" \"gray_bmp.png\",\n",
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" \"HCD1464653.qsdr.fz\",\n",
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"]\n",
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"\n",
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"# Add the appropriate extensions\n",
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"files_to_download_modalities = []\n",
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"for img in modalities_imgs:\n",
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" if (\n",
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" not img.endswith(\".png\")\n",
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" and not img.endswith(\".jpg\")\n",
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" and not img.endswith(\".fz\")\n",
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" ):\n",
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" img_with_ext = img + \".nii.gz\"\n",
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" else:\n",
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" img_with_ext = img\n",
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" files_to_download_modalities.append(img_with_ext)\n",
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"\n",
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"download_dataset(\n",
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" api_url=\"https://niivue.github.io/niivue-demo-images/\",\n",
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" dest_folder=DATA_FOLDER,\n",
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" files=files_to_download_modalities,\n",
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")"
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]
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},
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{
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"cell_type": "markdown",
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"id": "d17023b6-94dc-4a38-846a-719fcfaa7009",
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"metadata": {},
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"source": [
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"# Setup NiiVue Instance"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "14021983-a5fc-400b-b58c-1b9d0284d68b",
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"metadata": {},
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"outputs": [],
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"source": [
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"nv = NiiVue(\n",
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" back_color=(0.7, 0.7, 0.9, 1),\n",
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")\n",
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"nv.opts.is_colorbar = True\n",
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"nv.set_slice_type(\"RENDER\")\n",
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"nv.set_clip_plane(0.35, 270, 0)\n",
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"\n",
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"initial_volume_path = DATA_FOLDER / \"mni152.nii.gz\"\n",
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"nv.load_volumes(\n",
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" [\n",
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" {\n",
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" \"path\": initial_volume_path,\n",
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" \"colormap\": \"gray\",\n",
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" \"opacity\": 1,\n",
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" \"visible\": True,\n",
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" }\n",
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" ]\n",
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")"
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]
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},
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{
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"cell_type": "markdown",
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"id": "ba2edb7f-fa9f-4194-aad5-c74cfb0fffdb",
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"metadata": {},
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"source": [
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"# Store image paths"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "38e81fe1-0afc-4391-bc7b-b07e72739171",
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"metadata": {},
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"outputs": [],
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"source": [
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"img_paths = {}\n",
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"\n",
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"# Formats\n",
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"for img in local_imgs:\n",
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" img_path = DATA_FOLDER / img\n",
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" img_paths[img] = img_path\n",
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" if img.endswith(\".HEAD\"):\n",
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" # Also map the paired .BRIK file\n",
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" brik_file = img.replace(\".HEAD\", \".BRIK\")\n",
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" brik_path = DATA_FOLDER / brik_file\n",
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" img_paths[img + \"_paired\"] = brik_path\n",
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"\n",
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"# Modalities\n",
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"for img in modalities_imgs:\n",
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" if (\n",
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" not img.endswith(\".png\")\n",
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" and not img.endswith(\".jpg\")\n",
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" and not img.endswith(\".fz\")\n",
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" ):\n",
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" img_with_ext = img + \".nii.gz\"\n",
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" else:\n",
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" img_with_ext = img\n",
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" img_path = DATA_FOLDER / img_with_ext\n",
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" img_paths[img] = img_path"
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]
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},
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{
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"cell_type": "markdown",
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"id": "bc147316-9433-4e13-ac92-6e1dbc9143dc",
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"metadata": {},
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"source": [
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"# Dropdowns"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "4c85aff2-40d0-439b-a581-32b0bfab9316",
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"metadata": {},
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"outputs": [],
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"source": [
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"# Dropdown for Formats\n",
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"formats_dropdown = widgets.Dropdown(\n",
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" options=[(img, img) for img in local_imgs],\n",
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" description=\"Formats:\",\n",
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" value=None,\n",
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")\n",
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"\n",
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"# Dropdown for Modalities\n",
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"modalities_dropdown = widgets.Dropdown(\n",
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" options=[(img, img) for img in modalities_imgs],\n",
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" description=\"Modalities:\",\n",
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" value=None,\n",
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")\n",
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"\n",
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"# Dropdown for Colormaps\n",
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"colormaps = sorted(nv.colormaps())\n",
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"colormap_dropdown = widgets.Dropdown(\n",
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" options=colormaps,\n",
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" description=\"Colormap:\",\n",
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" value=\"gray\",\n",
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")"
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]
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},
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{
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"cell_type": "markdown",
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"id": "d96f552b-dc63-4fd6-ace8-653e1ef453fb",
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"metadata": {},
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"source": [
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"# Event handlers"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "bd2d2635-4faf-403e-b2d5-494422841601",
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"metadata": {},
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"outputs": [],
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"source": [
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"def on_format_change(change):\n",
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" \"\"\"Handle selection in Formats Dropdown.\"\"\"\n",
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" selected_img = change[\"new\"]\n",
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" if not selected_img:\n",
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" return\n",
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" img_path = img_paths.get(selected_img)\n",
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" if not img_path.exists():\n",
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" print(f\"Image {img_path} not found.\")\n",
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" return\n",
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" volumeObj = {\n",
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" \"path\": img_path,\n",
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" \"colormap\": \"gray\",\n",
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" \"opacity\": 1,\n",
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" \"visible\": True,\n",
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" }\n",
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" if selected_img.endswith(\".HEAD\"):\n",
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" paired_img_path = img_paths.get(selected_img + \"_paired\")\n",
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" if not paired_img_path or not paired_img_path.exists():\n",
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" print(f\"Paired image {paired_img_path} not found.\")\n",
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" return\n",
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" volumeObj[\"paired_img_path\"] = paired_img_path\n",
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" print(\"Loading format image:\", img_path.name)\n",
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" nv.load_volumes([volumeObj])\n",
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" # Reset Modalities Dropdown\n",
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" modalities_dropdown.unobserve(on_modality_change, names=\"value\")\n",
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" modalities_dropdown.value = None\n",
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" modalities_dropdown.observe(on_modality_change, names=\"value\")\n",
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" # Update colormap\n",
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" if nv.volumes:\n",
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" colormap_dropdown.value = nv.volumes[0].colormap\n",
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"\n",
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"\n",
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"def on_modality_change(change):\n",
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" \"\"\"Handle selection in Modalities Dropdown.\"\"\"\n",
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" selected_img = change[\"new\"]\n",
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" if not selected_img:\n",
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" return\n",
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" img_path = img_paths.get(selected_img)\n",
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" if not img_path.exists():\n",
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" print(f\"Image {img_path} not found.\")\n",
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" return\n",
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" volumeObj = {\n",
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" \"path\": img_path,\n",
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" \"colormap\": \"gray\",\n",
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" \"opacity\": 1,\n",
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" \"visible\": True,\n",
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" }\n",
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" print(\"Loading modality image:\", img_path.name)\n",
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" nv.load_volumes([volumeObj])\n",
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" # Reset Formats Dropdown\n",
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" formats_dropdown.unobserve(on_format_change, names=\"value\")\n",
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" formats_dropdown.value = None\n",
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" formats_dropdown.observe(on_format_change, names=\"value\")\n",
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" # Update colormap\n",
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" if nv.volumes:\n",
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" colormap_dropdown.value = nv.volumes[0].colormap\n",
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"\n",
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"\n",
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"def on_colormap_change(change):\n",
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" \"\"\"Handle selection in Colormap Dropdown.\"\"\"\n",
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" selected_cmap = change[\"new\"]\n",
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" if nv.volumes:\n",
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" nv.set_colormap(nv.volumes[0].id, selected_cmap)"
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]
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},
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{
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"cell_type": "markdown",
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"id": "70b2b439-11c0-411b-9378-5df96be084ad",
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"metadata": {},
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"source": [
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"# Observe the dropdowns"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "d9ee4730-6b3c-45a6-a664-a873e667fe67",
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"metadata": {},
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"outputs": [],
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"source": [
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"formats_dropdown.observe(on_format_change, names=\"value\")\n",
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"modalities_dropdown.observe(on_modality_change, names=\"value\")\n",
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"colormap_dropdown.observe(on_colormap_change, names=\"value\")"
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]
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},
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{
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"cell_type": "markdown",
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"id": "416fe1dd-4179-4d58-afbd-2799ea4eba03",
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"metadata": {},
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"source": [
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"# Display all"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "0b107556-61a3-4581-ac77-e2c21a26883b",
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"metadata": {},
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"outputs": [],
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"source": [
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"controls = widgets.VBox(\n",
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" [\n",
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" formats_dropdown,\n",
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" modalities_dropdown,\n",
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" colormap_dropdown,\n",
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" ]\n",
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")\n",
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"\n",
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"display(controls, nv)"
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]
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}
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],
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"metadata": {},
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"nbformat": 4,
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"nbformat_minor": 5
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}

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