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Merge pull request #303 from clEsperanto/test
Test inf-sup with morphological snakes
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,262 @@ | ||
| { | ||
| "cells": [ | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "e535dc08-1602-4ad0-9b79-db9a8a4b607f", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "# Pyclesperanto on Apple M1 CPUs/GPUs\n", | ||
| "This notebook serves exploring and basic benchmarking of CPUs and GPUs in an Apple M1 laptop" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 1, | ||
| "id": "4bb88b1a-2e9a-463f-9b3f-095d7766e9b8", | ||
| "metadata": {}, | ||
| "outputs": [ | ||
| { | ||
| "data": { | ||
| "text/plain": [ | ||
| "['Apple M1 Max', 'Apple M1 Max']" | ||
| ] | ||
| }, | ||
| "execution_count": 1, | ||
| "metadata": {}, | ||
| "output_type": "execute_result" | ||
| } | ||
| ], | ||
| "source": [ | ||
| "import numpy as np\n", | ||
| "import napari_segment_blobs_and_things_with_membranes as nsbatwm\n", | ||
| "import timeit\n", | ||
| "import pyclesperanto_prototype as cle\n", | ||
| "cle.available_device_names()" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "105c5a7f-6b94-44bc-a4a5-b1bbbfa6577a", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "## Defining test data\n" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 2, | ||
| "id": "d96117ce-5312-477d-a646-04db49204dce", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "image = np.random.random((2048, 2048))\n", | ||
| "\n", | ||
| "sigma_spot_detection = 1\n", | ||
| "sigma_outline = 1" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "c64a6c88-5eaa-43e6-95e0-d7170c6ae9a8", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "## M1 CPU" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 3, | ||
| "id": "4f9a4565-fe00-4f52-a7d6-92e6592ca11c", | ||
| "metadata": {}, | ||
| "outputs": [ | ||
| { | ||
| "data": { | ||
| "text/plain": [ | ||
| "<Apple M1 Max on Platform: Apple (2 refs)>" | ||
| ] | ||
| }, | ||
| "execution_count": 3, | ||
| "metadata": {}, | ||
| "output_type": "execute_result" | ||
| } | ||
| ], | ||
| "source": [ | ||
| "device = cle.select_device(dev_type='cpu')\n", | ||
| "device" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 4, | ||
| "id": "527744b1-a87a-41c6-9fec-876cf373f6c2", | ||
| "metadata": {}, | ||
| "outputs": [ | ||
| { | ||
| "data": { | ||
| "text/plain": [ | ||
| "2" | ||
| ] | ||
| }, | ||
| "execution_count": 4, | ||
| "metadata": {}, | ||
| "output_type": "execute_result" | ||
| } | ||
| ], | ||
| "source": [ | ||
| "device.device.type" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 5, | ||
| "id": "9dedb68c-4894-41ca-9aca-e62c45fae3ca", | ||
| "metadata": {}, | ||
| "outputs": [ | ||
| { | ||
| "name": "stdout", | ||
| "output_type": "stream", | ||
| "text": [ | ||
| "614 ms ± 6.92 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)\n" | ||
| ] | ||
| } | ||
| ], | ||
| "source": [ | ||
| "%timeit nsbatwm.voronoi_otsu_labeling(image, spot_sigma=sigma_spot_detection, outline_sigma=sigma_outline)\n" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 6, | ||
| "id": "3e082fb5-b05d-4c43-9df2-148b4dd856f7", | ||
| "metadata": {}, | ||
| "outputs": [ | ||
| { | ||
| "name": "stdout", | ||
| "output_type": "stream", | ||
| "text": [ | ||
| "530 ms ± 5.04 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)\n" | ||
| ] | ||
| } | ||
| ], | ||
| "source": [ | ||
| "%timeit cle.voronoi_otsu_labeling(image, spot_sigma=sigma_spot_detection, outline_sigma=sigma_outline)\n" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "fc839892-799a-478a-8630-e08799abb7dd", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "## M1 GPU" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 7, | ||
| "id": "596a9fd6-6c16-4ac1-baf2-c1632927281a", | ||
| "metadata": {}, | ||
| "outputs": [ | ||
| { | ||
| "data": { | ||
| "text/plain": [ | ||
| "<Apple M1 Max on Platform: Apple (2 refs)>" | ||
| ] | ||
| }, | ||
| "execution_count": 7, | ||
| "metadata": {}, | ||
| "output_type": "execute_result" | ||
| } | ||
| ], | ||
| "source": [ | ||
| "device = cle.select_device(dev_type='gpu')\n", | ||
| "device" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 8, | ||
| "id": "9b6c2628-a583-43c2-8efb-0ff258f88e45", | ||
| "metadata": {}, | ||
| "outputs": [ | ||
| { | ||
| "data": { | ||
| "text/plain": [ | ||
| "4" | ||
| ] | ||
| }, | ||
| "execution_count": 8, | ||
| "metadata": {}, | ||
| "output_type": "execute_result" | ||
| } | ||
| ], | ||
| "source": [ | ||
| "device.device.type" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 9, | ||
| "id": "be410bc8-2e74-4a15-9ce9-60c80e3caf4c", | ||
| "metadata": {}, | ||
| "outputs": [ | ||
| { | ||
| "name": "stdout", | ||
| "output_type": "stream", | ||
| "text": [ | ||
| "609 ms ± 3.63 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)\n" | ||
| ] | ||
| } | ||
| ], | ||
| "source": [ | ||
| "%timeit nsbatwm.voronoi_otsu_labeling(image, spot_sigma=sigma_spot_detection, outline_sigma=sigma_outline)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 10, | ||
| "id": "6d655aed-44f2-42c4-ae10-fb22f8c31232", | ||
| "metadata": {}, | ||
| "outputs": [ | ||
| { | ||
| "name": "stdout", | ||
| "output_type": "stream", | ||
| "text": [ | ||
| "609 ms ± 4.32 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)\n" | ||
| ] | ||
| } | ||
| ], | ||
| "source": [ | ||
| "%timeit nsbatwm.voronoi_otsu_labeling(image, spot_sigma=sigma_spot_detection, outline_sigma=sigma_outline)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "id": "aa036230-428c-495c-a933-0beaf600915c", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [] | ||
| } | ||
| ], | ||
| "metadata": { | ||
| "kernelspec": { | ||
| "display_name": "Python 3 (ipykernel)", | ||
| "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": "3.9.0" | ||
| } | ||
| }, | ||
| "nbformat": 4, | ||
| "nbformat_minor": 5 | ||
| } |
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