situr/notebook/tile_demo_test.ipynb

{
    "cells": [
        {
            "cell_type": "code",
            "execution_count": 4,
            "source": [
                "from situr.image import Tile\n",
                "from situr.registration import PeakFinderDifferenceOfGaussian\n",
                "from situr.registration import CombinedRegistration, AllChannelRoundRegistration, ChannelRegistration\n",
                "from PIL import Image\n"
            ],
            "outputs": [],
            "metadata": {}
        },
        {
            "cell_type": "code",
            "execution_count": 5,
            "source": [
                "round_list = [[['./artificial_img/original.tif']], [['./artificial_img/rotated.tif']]]"
            ],
            "outputs": [],
            "metadata": {}
        },
        {
            "cell_type": "code",
            "execution_count": 6,
            "source": [
                "tile = Tile(round_list)\n",
                "tile.to_numpy_array().shape"
            ],
            "outputs": [
                {
                    "output_type": "execute_result",
                    "data": {
                        "text/plain": [
                            "(2, 1, 1, 2048, 2048)"
                        ]
                    },
                    "metadata": {},
                    "execution_count": 6
                }
            ],
            "metadata": {}
        },
        {
            "cell_type": "code",
            "execution_count": 7,
            "source": [
                "peak_finder = PeakFinderDifferenceOfGaussian()\n",
                "registration = CombinedRegistration(AllChannelRoundRegistration(peak_finder=peak_finder), ChannelRegistration(peak_finder=peak_finder))\n",
                "registration.do_registration_and_transform(tile)"
            ],
            "outputs": [],
            "metadata": {}
        },
        {
            "cell_type": "code",
            "execution_count": 8,
            "source": [
                "peak_finder.show_channel_peaks(tile.get_round(0), 0, img_show=False)"
            ],
            "outputs": [
                {
                    "output_type": "execute_result",
                    "data": {
                        "text/plain": [
                            "<PIL.Image.Image image mode=RGB size=2048x2048 at 0x7FCF5411D070>"
                        ],
                        "image/png": 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                    },
                    "metadata": {},
                    "execution_count": 8
                }
            ],
            "metadata": {}
        },
        {
            "cell_type": "code",
            "execution_count": 9,
            "source": [
                "peak_finder.show_channel_peaks(tile.get_round(1), 0, img_show=False)"
            ],
            "outputs": [
                {
                    "output_type": "execute_result",
                    "data": {
                        "text/plain": [
                            "<PIL.Image.Image image mode=RGB size=2048x2048 at 0x7FCEE87BD6A0>"
                        ],
                        "image/png": 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