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November 4, 2021 21:47
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open_ims_from_julia.ipynb
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| { | |
| "cells": [ | |
| { | |
| "cell_type": "code", | |
| "execution_count": 1, | |
| "id": "excess-omega", | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "name": "stdout", | |
| "output_type": "stream", | |
| "text": [ | |
| "Julia Version 1.6.3\n", | |
| "Commit ae8452a9e0 (2021-09-23 17:34 UTC)\n", | |
| "Platform Info:\n", | |
| " OS: Windows (x86_64-w64-mingw32)\n", | |
| " CPU: Intel(R) Core(TM) i9-9880H CPU @ 2.30GHz\n", | |
| " WORD_SIZE: 64\n", | |
| " LIBM: libopenlibm\n", | |
| " LLVM: libLLVM-11.0.1 (ORCJIT, skylake)\n" | |
| ] | |
| } | |
| ], | |
| "source": [ | |
| "versioninfo()" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 2, | |
| "id": "initial-arrow", | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "name": "stderr", | |
| "output_type": "stream", | |
| "text": [ | |
| "\u001b[32m\u001b[1m Activating\u001b[22m\u001b[39m environment at `C:\\Users\\kittisopikulm\\Documents\\Keller_Lab\\HDF5Demo\\Project.toml`\n" | |
| ] | |
| }, | |
| { | |
| "name": "stdout", | |
| "output_type": "stream", | |
| "text": [ | |
| "\u001b[32m\u001b[1m Status\u001b[22m\u001b[39m `C:\\Users\\kittisopikulm\\Documents\\Keller_Lab\\HDF5Demo\\Project.toml` (empty project)\n" | |
| ] | |
| } | |
| ], | |
| "source": [ | |
| "using Pkg\n", | |
| "Pkg.activate(\"HDF5Demo\")\n", | |
| "Pkg.status()" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 4, | |
| "id": "sunrise-component", | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [ | |
| "# For testing\n", | |
| "#Pkg.rm([\"HDF5\",\"HDF5Plugins\"])" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 6, | |
| "id": "champion-calcium", | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [ | |
| "try\n", | |
| " using HDF5\n", | |
| " using HDF5Plugins\n", | |
| "catch err\n", | |
| " Pkg.add([\"HDF5\", \"HDF5Plugins\"])\n", | |
| " using HDF5\n", | |
| " using HDF5Plugins\n", | |
| "end" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 7, | |
| "id": "published-norway", | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "data": { | |
| "text/plain": [ | |
| "\"C:\\\\Users\\\\kittisopikulm\\\\.julia\\\\dev\\\\HDF5\\\\out_0.ims\"" | |
| ] | |
| }, | |
| "execution_count": 7, | |
| "metadata": {}, | |
| "output_type": "execute_result" | |
| } | |
| ], | |
| "source": [ | |
| "imsfile = raw\"C:\\Users\\kittisopikulm\\.julia\\dev\\HDF5\\out_0.ims\" # From ImarisWriterTest" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 8, | |
| "id": "pediatric-saver", | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "data": { | |
| "text/plain": [ | |
| "🗂️ HDF5.File: (read-only) C:\\Users\\kittisopikulm\\.julia\\dev\\HDF5\\out_0.ims\n", | |
| "├─ 🏷️ DataSetDirectoryName\n", | |
| "├─ 🏷️ DataSetInfoDirectoryName\n", | |
| "├─ 🏷️ ImarisDataSet\n", | |
| "├─ 🏷️ ImarisVersion\n", | |
| "├─ 🏷️ NumberOfDataSets\n", | |
| "├─ 🏷️ ThumbnailDirectoryName\n", | |
| "├─ 📂 DataSet\n", | |
| "│ ├─ 📂 ResolutionLevel 0\n", | |
| "│ │ ├─ 📂 TimePoint 0\n", | |
| "│ │ │ ├─ 📂 Channel 0\n", | |
| "│ │ │ │ ├─ 🏷️ HistogramMax\n", | |
| "│ │ │ │ ├─ 🏷️ HistogramMin\n", | |
| "│ │ │ │ ├─ 🏷️ ImageSizeX\n", | |
| "│ │ │ │ ├─ 🏷️ ImageSizeY\n", | |
| "│ │ │ │ ├─ 🏷️ ImageSizeZ\n", | |
| "│ │ │ │ ├─ 🔢 Data\n", | |
| "│ │ │ │ └─ 🔢 Histogram\n", | |
| "│ │ │ ├─ 📂 Channel 1\n", | |
| "│ │ │ │ ├─ 🏷️ HistogramMax\n", | |
| "│ │ │ │ ├─ 🏷️ HistogramMin\n", | |
| "│ │ │ │ ├─ 🏷️ ImageSizeX\n", | |
| "│ │ │ │ ├─ 🏷️ ImageSizeY\n", | |
| "│ │ │ │ ├─ 🏷️ ImageSizeZ\n", | |
| "│ │ │ │ ├─ 🔢 Data\n", | |
| "│ │ │ │ └─ 🔢 Histogram\n", | |
| "│ │ │ ├─ 📂 Channel 2\n", | |
| "│ │ │ │ ├─ 🏷️ HistogramMax\n", | |
| "│ │ │ │ ├─ 🏷️ HistogramMin\n", | |
| "│ │ │ │ ├─ 🏷️ ImageSizeX\n", | |
| "│ │ │ │ ├─ 🏷️ ImageSizeY\n", | |
| "│ │ │ │ ├─ 🏷️ ImageSizeZ\n", | |
| "│ │ │ │ ├─ 🔢 Data\n", | |
| "│ │ │ │ └─ 🔢 Histogram\n", | |
| "│ │ │ └─ 📂 Channel 3\n", | |
| "│ │ │ ├─ 🏷️ HistogramMax\n", | |
| "│ │ │ ├─ 🏷️ HistogramMin\n", | |
| "│ │ │ ├─ 🏷️ ImageSizeX\n", | |
| "│ │ │ ├─ 🏷️ ImageSizeY\n", | |
| "│ │ │ ├─ 🏷️ ImageSizeZ\n", | |
| "│ │ │ ├─ 🔢 Data\n", | |
| "│ │ │ └─ 🔢 Histogram\n", | |
| "│ │ └─ 📂 TimePoint 1\n", | |
| "│ │ ├─ 📂 Channel 0\n", | |
| "│ │ │ ├─ 🏷️ HistogramMax\n", | |
| "│ │ │ ├─ 🏷️ HistogramMin\n", | |
| "│ │ │ ├─ 🏷️ ImageSizeX\n", | |
| "│ │ │ ├─ 🏷️ ImageSizeY\n", | |
| "│ │ │ ├─ 🏷️ ImageSizeZ\n", | |
| "│ │ │ ├─ 🔢 Data\n", | |
| "│ │ │ └─ 🔢 Histogram\n", | |
| "│ │ ├─ 📂 Channel 1\n", | |
| "│ │ │ ├─ 🏷️ HistogramMax\n", | |
| "│ │ │ ├─ 🏷️ HistogramMin\n", | |
| "│ │ │ ├─ 🏷️ ImageSizeX\n", | |
| "│ │ │ ├─ 🏷️ ImageSizeY\n", | |
| "│ │ │ ├─ 🏷️ ImageSizeZ\n", | |
| "│ │ │ ├─ 🔢 Data\n", | |
| "│ │ │ └─ 🔢 Histogram\n", | |
| "│ │ ├─ 📂 Channel 2\n", | |
| "│ │ │ ├─ 🏷️ HistogramMax\n", | |
| "│ │ │ ├─ 🏷️ HistogramMin\n", | |
| "│ │ │ ├─ 🏷️ ImageSizeX\n", | |
| "│ │ │ ├─ 🏷️ ImageSizeY\n", | |
| "│ │ │ ├─ 🏷️ ImageSizeZ\n", | |
| "│ │ │ ├─ 🔢 Data\n", | |
| "│ │ │ └─ 🔢 Histogram\n", | |
| "│ │ └─ 📂 Channel 3\n", | |
| "│ │ ├─ 🏷️ HistogramMax\n", | |
| "│ │ ├─ 🏷️ HistogramMin\n", | |
| "│ │ ├─ 🏷️ ImageSizeX\n", | |
| "│ │ ├─ 🏷️ ImageSizeY\n", | |
| "│ │ ├─ 🏷️ ImageSizeZ\n", | |
| "│ │ ├─ 🔢 Data\n", | |
| "│ │ └─ 🔢 Histogram\n", | |
| "│ ├─ 📂 ResolutionLevel 1\n", | |
| "│ │ ├─ 📂 TimePoint 0\n", | |
| "│ │ │ ├─ 📂 Channel 0\n", | |
| "│ │ │ │ ├─ 🏷️ HistogramMax\n", | |
| "│ │ │ │ ├─ 🏷️ HistogramMin\n", | |
| "│ │ │ │ ├─ 🏷️ ImageSizeX\n", | |
| "│ │ │ │ ├─ 🏷️ ImageSizeY\n", | |
| "│ │ │ │ ├─ 🏷️ ImageSizeZ\n", | |
| "│ │ │ │ ├─ 🔢 Data\n", | |
| "│ │ │ │ └─ 🔢 Histogram\n", | |
| "│ │ │ ├─ 📂 Channel 1\n", | |
| "│ │ │ │ ├─ 🏷️ HistogramMax\n", | |
| "│ │ │ │ ├─ 🏷️ HistogramMin\n", | |
| "│ │ │ │ ├─ 🏷️ ImageSizeX\n", | |
| "│ │ │ │ ├─ 🏷️ ImageSizeY\n", | |
| "│ │ │ │ ├─ 🏷️ ImageSizeZ\n", | |
| "│ │ │ │ ├─ 🔢 Data\n", | |
| "│ │ │ │ └─ 🔢 Histogram\n", | |
| "│ │ │ ├─ 📂 Channel 2\n", | |
| "│ │ │ │ ├─ 🏷️ HistogramMax\n", | |
| "│ │ │ │ ├─ 🏷️ HistogramMin\n", | |
| "│ │ │ │ ├─ 🏷️ ImageSizeX\n", | |
| "│ │ │ │ ├─ 🏷️ ImageSizeY\n", | |
| "│ │ │ │ ├─ 🏷️ ImageSizeZ\n", | |
| "│ │ │ │ ├─ 🔢 Data\n", | |
| "│ │ │ │ └─ 🔢 Histogram\n", | |
| "│ │ │ └─ 📂 Channel 3\n", | |
| "│ │ │ ├─ 🏷️ HistogramMax\n", | |
| "│ │ │ ├─ 🏷️ HistogramMin\n", | |
| "│ │ │ ├─ 🏷️ ImageSizeX\n", | |
| "│ │ │ ├─ 🏷️ ImageSizeY\n", | |
| "│ │ │ ├─ 🏷️ ImageSizeZ\n", | |
| "│ │ │ ├─ 🔢 Data\n", | |
| "│ │ │ └─ 🔢 Histogram\n", | |
| "│ │ └─ 📂 TimePoint 1\n", | |
| "│ │ ├─ 📂 Channel 0\n", | |
| "│ │ │ ├─ 🏷️ HistogramMax\n", | |
| "│ │ │ ├─ 🏷️ HistogramMin\n", | |
| "│ │ │ ├─ 🏷️ ImageSizeX\n", | |
| "│ │ │ ├─ 🏷️ ImageSizeY\n", | |
| "│ │ │ ├─ 🏷️ ImageSizeZ\n", | |
| "│ │ │ ├─ 🔢 Data\n", | |
| "│ │ │ └─ 🔢 Histogram\n", | |
| "│ │ ├─ 📂 Channel 1\n", | |
| "│ │ │ ├─ 🏷️ HistogramMax\n", | |
| "│ │ │ ├─ 🏷️ HistogramMin\n", | |
| "│ │ │ ├─ 🏷️ ImageSizeX\n", | |
| "│ │ │ ├─ 🏷️ ImageSizeY\n", | |
| "│ │ │ ├─ 🏷️ ImageSizeZ\n", | |
| "│ │ │ ├─ 🔢 Data\n", | |
| "│ │ │ └─ 🔢 Histogram\n", | |
| "│ │ ├─ 📂 Channel 2\n", | |
| "│ │ │ ├─ 🏷️ HistogramMax\n", | |
| "│ │ │ ├─ 🏷️ HistogramMin\n", | |
| "│ │ │ ├─ 🏷️ ImageSizeX\n", | |
| "│ │ │ ├─ 🏷️ ImageSizeY\n", | |
| "│ │ │ ├─ 🏷️ ImageSizeZ\n", | |
| "│ │ │ ├─ 🔢 Data\n", | |
| "│ │ │ └─ 🔢 Histogram\n", | |
| "│ │ └─ 📂 Channel 3\n", | |
| "│ │ ├─ 🏷️ HistogramMax\n", | |
| "│ │ ├─ 🏷️ HistogramMin\n", | |
| "│ │ ├─ 🏷️ ImageSizeX\n", | |
| "│ │ ├─ 🏷️ ImageSizeY\n", | |
| "│ │ ├─ 🏷️ ImageSizeZ\n", | |
| "│ │ ├─ 🔢 Data\n", | |
| "│ │ └─ 🔢 Histogram\n", | |
| "│ └─ 📂 ResolutionLevel 2\n", | |
| "│ ├─ 📂 TimePoint 0\n", | |
| "│ │ ├─ 📂 Channel 0\n", | |
| "│ │ │ ├─ 🏷️ HistogramMax\n", | |
| "│ │ │ ├─ 🏷️ HistogramMin\n", | |
| "│ │ │ ├─ 🏷️ ImageSizeX\n", | |
| "│ │ │ ├─ 🏷️ ImageSizeY\n", | |
| "│ │ │ ├─ 🏷️ ImageSizeZ\n", | |
| "│ │ │ ├─ 🔢 Data\n", | |
| "│ │ │ └─ 🔢 Histogram\n", | |
| "│ │ ├─ 📂 Channel 1\n", | |
| "│ │ │ ├─ 🏷️ HistogramMax\n", | |
| "│ │ │ ├─ 🏷️ HistogramMin\n", | |
| "│ │ │ ├─ 🏷️ ImageSizeX\n", | |
| "│ │ │ ├─ 🏷️ ImageSizeY\n", | |
| "│ │ │ ├─ 🏷️ ImageSizeZ\n", | |
| "│ │ │ ├─ 🔢 Data\n", | |
| "│ │ │ └─ 🔢 Histogram\n", | |
| "│ │ ├─ 📂 Channel 2\n", | |
| "│ │ │ ├─ 🏷️ HistogramMax\n", | |
| "│ │ │ ├─ 🏷️ HistogramMin\n", | |
| "│ │ │ ├─ 🏷️ ImageSizeX\n", | |
| "│ │ │ ├─ 🏷️ ImageSizeY\n", | |
| "│ │ │ ├─ 🏷️ ImageSizeZ\n", | |
| "│ │ │ ├─ 🔢 Data\n", | |
| "│ │ │ └─ 🔢 Histogram\n", | |
| "│ │ └─ 📂 Channel 3\n", | |
| "│ │ ├─ 🏷️ HistogramMax\n", | |
| "│ │ ├─ 🏷️ HistogramMin\n", | |
| "│ │ ├─ 🏷️ ImageSizeX\n", | |
| "│ │ ├─ 🏷️ ImageSizeY\n", | |
| "│ │ ├─ 🏷️ ImageSizeZ\n", | |
| "│ │ ├─ 🔢 Data\n", | |
| "│ │ └─ 🔢 Histogram\n", | |
| "│ └─ 📂 TimePoint 1\n", | |
| "│ ├─ 📂 Channel 0\n", | |
| "│ │ ├─ 🏷️ HistogramMax\n", | |
| "│ │ ├─ 🏷️ HistogramMin\n", | |
| "│ │ ├─ 🏷️ ImageSizeX\n", | |
| "│ │ ├─ 🏷️ ImageSizeY\n", | |
| "│ │ ├─ 🏷️ ImageSizeZ\n", | |
| "│ │ ├─ 🔢 Data\n", | |
| "│ │ └─ 🔢 Histogram\n", | |
| "│ ├─ 📂 Channel 1\n", | |
| "│ │ ├─ 🏷️ HistogramMax\n", | |
| "│ │ ├─ 🏷️ HistogramMin\n", | |
| "│ │ ├─ 🏷️ ImageSizeX\n", | |
| "│ │ ├─ 🏷️ ImageSizeY\n", | |
| "│ │ ├─ 🏷️ ImageSizeZ\n", | |
| "│ │ ├─ 🔢 Data\n", | |
| "│ │ └─ 🔢 Histogram\n", | |
| "│ ├─ 📂 Channel 2\n", | |
| "│ │ ├─ 🏷️ HistogramMax\n", | |
| "│ │ ├─ 🏷️ HistogramMin\n", | |
| "│ │ ├─ 🏷️ ImageSizeX\n", | |
| "│ │ ├─ 🏷️ ImageSizeY\n", | |
| "│ │ ├─ 🏷️ ImageSizeZ\n", | |
| "│ │ ├─ 🔢 Data\n", | |
| "│ │ └─ 🔢 Histogram\n", | |
| "│ └─ 📂 Channel 3\n", | |
| "│ ├─ 🏷️ HistogramMax\n", | |
| "│ ├─ 🏷️ HistogramMin\n", | |
| "│ ├─ 🏷️ ImageSizeX\n", | |
| "│ ├─ 🏷️ ImageSizeY\n", | |
| "│ ├─ 🏷️ ImageSizeZ\n", | |
| "│ ├─ 🔢 Data\n", | |
| "│ └─ 🔢 Histogram\n", | |
| "├─ 📂 DataSetInfo\n", | |
| "│ ├─ 📂 Channel 0\n", | |
| "│ │ ├─ 🏷️ Color\n", | |
| "│ │ ├─ 🏷️ ColorMode\n", | |
| "│ │ ├─ 🏷️ ColorOpacity\n", | |
| "│ │ ├─ 🏷️ ColorRange\n", | |
| "│ │ ├─ 🏷️ Description\n", | |
| "│ │ ├─ 🏷️ GammaCorrection\n", | |
| "│ │ └─ 🏷️ Name\n", | |
| "│ ├─ 📂 Channel 1\n", | |
| "│ │ ├─ 🏷️ Color\n", | |
| "│ │ ├─ 🏷️ ColorMode\n", | |
| "│ │ ├─ 🏷️ ColorOpacity\n", | |
| "│ │ ├─ 🏷️ ColorRange\n", | |
| "│ │ ├─ 🏷️ Description\n", | |
| "│ │ ├─ 🏷️ GammaCorrection\n", | |
| "│ │ ├─ 🏷️ LSMEmissionWavelength\n", | |
| "│ │ ├─ 🏷️ Name\n", | |
| "│ │ └─ 🏷️ OtherChannelParameter\n", | |
| "│ ├─ 📂 Channel 2\n", | |
| "│ │ ├─ 🏷️ Color\n", | |
| "│ │ ├─ 🏷️ ColorMode\n", | |
| "│ │ ├─ 🏷️ ColorOpacity\n", | |
| "│ │ ├─ 🏷️ ColorRange\n", | |
| "│ │ ├─ 🏷️ Description\n", | |
| "│ │ ├─ 🏷️ GammaCorrection\n", | |
| "│ │ ├─ 🏷️ LSMEmissionWavelength\n", | |
| "│ │ ├─ 🏷️ Name\n", | |
| "│ │ └─ 🏷️ OtherChannelParameter\n", | |
| "│ ├─ 📂 Channel 3\n", | |
| "│ │ ├─ 🏷️ Color\n", | |
| "│ │ ├─ 🏷️ ColorMode\n", | |
| "│ │ ├─ 🏷️ ColorOpacity\n", | |
| "│ │ ├─ 🏷️ ColorRange\n", | |
| "│ │ ├─ 🏷️ Description\n", | |
| "│ │ ├─ 🏷️ GammaCorrection\n", | |
| "│ │ ├─ 🏷️ LSMEmissionWavelength\n", | |
| "│ │ ├─ 🏷️ Name\n", | |
| "│ │ └─ 🏷️ OtherChannelParameter\n", | |
| "│ ├─ 📂 Channel 4\n", | |
| "│ │ ├─ 🏷️ LSMEmissionWavelength\n", | |
| "│ │ ├─ 🏷️ Name\n", | |
| "│ │ └─ 🏷️ OtherChannelParameter\n", | |
| "│ ├─ 📂 Image\n", | |
| "│ │ ├─ 🏷️ Description\n", | |
| "│ │ ├─ 🏷️ ExtMax0\n", | |
| "│ │ ├─ 🏷️ ExtMax1\n", | |
| "│ │ ├─ 🏷️ ExtMax2\n", | |
| "│ │ ├─ 🏷️ ExtMin0\n", | |
| "│ │ ├─ 🏷️ ExtMin1\n", | |
| "│ │ ├─ 🏷️ ExtMin2\n", | |
| "│ │ ├─ 🏷️ Name\n", | |
| "│ │ ├─ 🏷️ RecordingDate\n", | |
| "│ │ ├─ 🏷️ ResampleDimensionX\n", | |
| "│ │ ├─ 🏷️ ResampleDimensionY\n", | |
| "│ │ ├─ 🏷️ ResampleDimensionZ\n", | |
| "│ │ ├─ 🏷️ Unit\n", | |
| "│ │ ├─ 🏷️ X\n", | |
| "│ │ ├─ 🏷️ Y\n", | |
| "│ │ └─ 🏷️ Z\n", | |
| "│ ├─ 📂 ImarisDataSet\n", | |
| "│ │ ├─ 🏷️ Creator\n", | |
| "│ │ ├─ 🏷️ NumberOfImages\n", | |
| "│ │ └─ 🏷️ Version\n", | |
| "│ ├─ 📂 Log\n", | |
| "│ │ └─ 🏷️ Entries\n", | |
| "│ └─ 📂 TimeInfo\n", | |
| "│ ├─ 🏷️ DatasetTimePoints\n", | |
| "│ ├─ 🏷️ FileTimePoints\n", | |
| "│ ├─ 🏷️ TimePoint1\n", | |
| "│ └─ 🏷️ TimePoint2\n", | |
| "└─ 📂 Thumbnail\n", | |
| " └─ 🔢 Data" | |
| ] | |
| }, | |
| "execution_count": 8, | |
| "metadata": {}, | |
| "output_type": "execute_result" | |
| } | |
| ], | |
| "source": [ | |
| "h5file = h5open(imsfile)" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 9, | |
| "id": "distinguished-latvia", | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "data": { | |
| "text/plain": [ | |
| "📂 HDF5.Group: /DataSet/ResolutionLevel 0/TimePoint 0/Channel 0 (file: C:\\Users\\kittisopikulm\\.julia\\dev\\HDF5\\out_0.ims)\n", | |
| "├─ 🏷️ HistogramMax\n", | |
| "├─ 🏷️ HistogramMin\n", | |
| "├─ 🏷️ ImageSizeX\n", | |
| "├─ 🏷️ ImageSizeY\n", | |
| "├─ 🏷️ ImageSizeZ\n", | |
| "├─ 🔢 Data\n", | |
| "└─ 🔢 Histogram" | |
| ] | |
| }, | |
| "execution_count": 9, | |
| "metadata": {}, | |
| "output_type": "execute_result" | |
| } | |
| ], | |
| "source": [ | |
| "h5file[\"DataSet\"][\"ResolutionLevel 0\"][\"TimePoint 0\"][\"Channel 0\"]" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 10, | |
| "id": "gothic-comment", | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "data": { | |
| "text/plain": [ | |
| "HDF5.Group" | |
| ] | |
| }, | |
| "execution_count": 10, | |
| "metadata": {}, | |
| "output_type": "execute_result" | |
| } | |
| ], | |
| "source": [ | |
| "typeof(h5file[\"DataSet\"][\"ResolutionLevel 0\"][\"TimePoint 0\"][\"Channel 0\"])" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 11, | |
| "id": "focused-filing", | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "data": { | |
| "text/plain": [ | |
| "🔢 HDF5.Dataset: /DataSet/ResolutionLevel 0/TimePoint 0/Channel 0/Data (file: C:\\Users\\kittisopikulm\\.julia\\dev\\HDF5\\out_0.ims xfer_mode: 0)" | |
| ] | |
| }, | |
| "execution_count": 11, | |
| "metadata": {}, | |
| "output_type": "execute_result" | |
| } | |
| ], | |
| "source": [ | |
| "d = h5file[\"DataSet\"][\"ResolutionLevel 0\"][\"TimePoint 0\"][\"Channel 0\"][\"Data\"]" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 12, | |
| "id": "dominant-fetish", | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "data": { | |
| "text/plain": [ | |
| "3" | |
| ] | |
| }, | |
| "execution_count": 12, | |
| "metadata": {}, | |
| "output_type": "execute_result" | |
| } | |
| ], | |
| "source": [ | |
| "ndims(d)" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 13, | |
| "id": "optional-nursing", | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "data": { | |
| "text/plain": [ | |
| "(512, 512, 32)" | |
| ] | |
| }, | |
| "execution_count": 13, | |
| "metadata": {}, | |
| "output_type": "execute_result" | |
| } | |
| ], | |
| "source": [ | |
| "size(d)" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 14, | |
| "id": "nearby-karen", | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "data": { | |
| "text/plain": [ | |
| "512×512×32 Array{UInt8, 3}:\n", | |
| "[:, :, 1] =\n", | |
| " 0x00 0x00 0x00 0x00 0x00 0x00 … 0x00 0x00 0x00 0x00 0x00 0x00\n", | |
| " 0x01 0x01 0x01 0x01 0x01 0x01 0x01 0x01 0x01 0x01 0x01 0x01\n", | |
| " 0x02 0x02 0x02 0x02 0x02 0x02 0x02 0x02 0x02 0x02 0x02 0x02\n", | |
| " 0x03 0x03 0x03 0x03 0x03 0x03 0x03 0x03 0x03 0x03 0x03 0x03\n", | |
| " 0x04 0x04 0x04 0x04 0x04 0x04 0x04 0x04 0x04 0x04 0x04 0x04\n", | |
| " 0x05 0x05 0x05 0x05 0x05 0x05 … 0x05 0x05 0x05 0x05 0x05 0x05\n", | |
| " 0x06 0x06 0x06 0x06 0x06 0x06 0x06 0x06 0x06 0x06 0x06 0x06\n", | |
| " 0x07 0x07 0x07 0x07 0x07 0x07 0x07 0x07 0x07 0x07 0x07 0x07\n", | |
| " 0x08 0x08 0x08 0x08 0x08 0x08 0x08 0x08 0x08 0x08 0x08 0x08\n", | |
| " 0x09 0x09 0x09 0x09 0x09 0x09 0x09 0x09 0x09 0x09 0x09 0x09\n", | |
| " 0x0a 0x0a 0x0a 0x0a 0x0a 0x0a … 0x0a 0x0a 0x0a 0x0a 0x0a 0x0a\n", | |
| " 0x0b 0x0b 0x0b 0x0b 0x0b 0x0b 0x0b 0x0b 0x0b 0x0b 0x0b 0x0b\n", | |
| " 0x0c 0x0c 0x0c 0x0c 0x0c 0x0c 0x0c 0x0c 0x0c 0x0c 0x0c 0x0c\n", | |
| " ⋮ ⋮ ⋱ ⋮ \n", | |
| " 0xf4 0xf4 0xf4 0xf4 0xf4 0xf4 … 0xf4 0xf4 0xf4 0xf4 0xf4 0xf4\n", | |
| " 0xf5 0xf5 0xf5 0xf5 0xf5 0xf5 0xf5 0xf5 0xf5 0xf5 0xf5 0xf5\n", | |
| " 0xf6 0xf6 0xf6 0xf6 0xf6 0xf6 0xf6 0xf6 0xf6 0xf6 0xf6 0xf6\n", | |
| " 0xf7 0xf7 0xf7 0xf7 0xf7 0xf7 0xf7 0xf7 0xf7 0xf7 0xf7 0xf7\n", | |
| " 0xf8 0xf8 0xf8 0xf8 0xf8 0xf8 0xf8 0xf8 0xf8 0xf8 0xf8 0xf8\n", | |
| " 0xf9 0xf9 0xf9 0xf9 0xf9 0xf9 … 0xf9 0xf9 0xf9 0xf9 0xf9 0xf9\n", | |
| " 0xfa 0xfa 0xfa 0xfa 0xfa 0xfa 0xfa 0xfa 0xfa 0xfa 0xfa 0xfa\n", | |
| " 0xfb 0xfb 0xfb 0xfb 0xfb 0xfb 0xfb 0xfb 0xfb 0xfb 0xfb 0xfb\n", | |
| " 0xfc 0xfc 0xfc 0xfc 0xfc 0xfc 0xfc 0xfc 0xfc 0xfc 0xfc 0xfc\n", | |
| " 0xfd 0xfd 0xfd 0xfd 0xfd 0xfd 0xfd 0xfd 0xfd 0xfd 0xfd 0xfd\n", | |
| " 0xfe 0xfe 0xfe 0xfe 0xfe 0xfe … 0xfe 0xfe 0xfe 0xfe 0xfe 0xfe\n", | |
| " 0xff 0xff 0xff 0xff 0xff 0xff 0xff 0xff 0xff 0xff 0xff 0xff\n", | |
| "\n", | |
| "[:, :, 2] =\n", | |
| " 0x00 0x00 0x00 0x00 0x00 0x00 … 0x00 0x00 0x00 0x00 0x00 0x00\n", | |
| " 0x01 0x01 0x01 0x01 0x01 0x01 0x01 0x01 0x01 0x01 0x01 0x01\n", | |
| " 0x02 0x02 0x02 0x02 0x02 0x02 0x02 0x02 0x02 0x02 0x02 0x02\n", | |
| " 0x03 0x03 0x03 0x03 0x03 0x03 0x03 0x03 0x03 0x03 0x03 0x03\n", | |
| " 0x04 0x04 0x04 0x04 0x04 0x04 0x04 0x04 0x04 0x04 0x04 0x04\n", | |
| " 0x05 0x05 0x05 0x05 0x05 0x05 … 0x05 0x05 0x05 0x05 0x05 0x05\n", | |
| " 0x06 0x06 0x06 0x06 0x06 0x06 0x06 0x06 0x06 0x06 0x06 0x06\n", | |
| " 0x07 0x07 0x07 0x07 0x07 0x07 0x07 0x07 0x07 0x07 0x07 0x07\n", | |
| " 0x08 0x08 0x08 0x08 0x08 0x08 0x08 0x08 0x08 0x08 0x08 0x08\n", | |
| " 0x09 0x09 0x09 0x09 0x09 0x09 0x09 0x09 0x09 0x09 0x09 0x09\n", | |
| " 0x0a 0x0a 0x0a 0x0a 0x0a 0x0a … 0x0a 0x0a 0x0a 0x0a 0x0a 0x0a\n", | |
| " 0x0b 0x0b 0x0b 0x0b 0x0b 0x0b 0x0b 0x0b 0x0b 0x0b 0x0b 0x0b\n", | |
| " 0x0c 0x0c 0x0c 0x0c 0x0c 0x0c 0x0c 0x0c 0x0c 0x0c 0x0c 0x0c\n", | |
| " ⋮ ⋮ ⋱ ⋮ \n", | |
| " 0xf4 0xf4 0xf4 0xf4 0xf4 0xf4 … 0xf4 0xf4 0xf4 0xf4 0xf4 0xf4\n", | |
| " 0xf5 0xf5 0xf5 0xf5 0xf5 0xf5 0xf5 0xf5 0xf5 0xf5 0xf5 0xf5\n", | |
| " 0xf6 0xf6 0xf6 0xf6 0xf6 0xf6 0xf6 0xf6 0xf6 0xf6 0xf6 0xf6\n", | |
| " 0xf7 0xf7 0xf7 0xf7 0xf7 0xf7 0xf7 0xf7 0xf7 0xf7 0xf7 0xf7\n", | |
| " 0xf8 0xf8 0xf8 0xf8 0xf8 0xf8 0xf8 0xf8 0xf8 0xf8 0xf8 0xf8\n", | |
| " 0xf9 0xf9 0xf9 0xf9 0xf9 0xf9 … 0xf9 0xf9 0xf9 0xf9 0xf9 0xf9\n", | |
| " 0xfa 0xfa 0xfa 0xfa 0xfa 0xfa 0xfa 0xfa 0xfa 0xfa 0xfa 0xfa\n", | |
| " 0xfb 0xfb 0xfb 0xfb 0xfb 0xfb 0xfb 0xfb 0xfb 0xfb 0xfb 0xfb\n", | |
| " 0xfc 0xfc 0xfc 0xfc 0xfc 0xfc 0xfc 0xfc 0xfc 0xfc 0xfc 0xfc\n", | |
| " 0xfd 0xfd 0xfd 0xfd 0xfd 0xfd 0xfd 0xfd 0xfd 0xfd 0xfd 0xfd\n", | |
| " 0xfe 0xfe 0xfe 0xfe 0xfe 0xfe … 0xfe 0xfe 0xfe 0xfe 0xfe 0xfe\n", | |
| " 0xff 0xff 0xff 0xff 0xff 0xff 0xff 0xff 0xff 0xff 0xff 0xff\n", | |
| "\n", | |
| "[:, :, 3] =\n", | |
| " 0x00 0x00 0x00 0x00 0x00 0x00 … 0x00 0x00 0x00 0x00 0x00 0x00\n", | |
| " 0x01 0x01 0x01 0x01 0x01 0x01 0x01 0x01 0x01 0x01 0x01 0x01\n", | |
| " 0x02 0x02 0x02 0x02 0x02 0x02 0x02 0x02 0x02 0x02 0x02 0x02\n", | |
| " 0x03 0x03 0x03 0x03 0x03 0x03 0x03 0x03 0x03 0x03 0x03 0x03\n", | |
| " 0x04 0x04 0x04 0x04 0x04 0x04 0x04 0x04 0x04 0x04 0x04 0x04\n", | |
| " 0x05 0x05 0x05 0x05 0x05 0x05 … 0x05 0x05 0x05 0x05 0x05 0x05\n", | |
| " 0x06 0x06 0x06 0x06 0x06 0x06 0x06 0x06 0x06 0x06 0x06 0x06\n", | |
| " 0x07 0x07 0x07 0x07 0x07 0x07 0x07 0x07 0x07 0x07 0x07 0x07\n", | |
| " 0x08 0x08 0x08 0x08 0x08 0x08 0x08 0x08 0x08 0x08 0x08 0x08\n", | |
| " 0x09 0x09 0x09 0x09 0x09 0x09 0x09 0x09 0x09 0x09 0x09 0x09\n", | |
| " 0x0a 0x0a 0x0a 0x0a 0x0a 0x0a … 0x0a 0x0a 0x0a 0x0a 0x0a 0x0a\n", | |
| " 0x0b 0x0b 0x0b 0x0b 0x0b 0x0b 0x0b 0x0b 0x0b 0x0b 0x0b 0x0b\n", | |
| " 0x0c 0x0c 0x0c 0x0c 0x0c 0x0c 0x0c 0x0c 0x0c 0x0c 0x0c 0x0c\n", | |
| " ⋮ ⋮ ⋱ ⋮ \n", | |
| " 0xf4 0xf4 0xf4 0xf4 0xf4 0xf4 … 0xf4 0xf4 0xf4 0xf4 0xf4 0xf4\n", | |
| " 0xf5 0xf5 0xf5 0xf5 0xf5 0xf5 0xf5 0xf5 0xf5 0xf5 0xf5 0xf5\n", | |
| " 0xf6 0xf6 0xf6 0xf6 0xf6 0xf6 0xf6 0xf6 0xf6 0xf6 0xf6 0xf6\n", | |
| " 0xf7 0xf7 0xf7 0xf7 0xf7 0xf7 0xf7 0xf7 0xf7 0xf7 0xf7 0xf7\n", | |
| " 0xf8 0xf8 0xf8 0xf8 0xf8 0xf8 0xf8 0xf8 0xf8 0xf8 0xf8 0xf8\n", | |
| " 0xf9 0xf9 0xf9 0xf9 0xf9 0xf9 … 0xf9 0xf9 0xf9 0xf9 0xf9 0xf9\n", | |
| " 0xfa 0xfa 0xfa 0xfa 0xfa 0xfa 0xfa 0xfa 0xfa 0xfa 0xfa 0xfa\n", | |
| " 0xfb 0xfb 0xfb 0xfb 0xfb 0xfb 0xfb 0xfb 0xfb 0xfb 0xfb 0xfb\n", | |
| " 0xfc 0xfc 0xfc 0xfc 0xfc 0xfc 0xfc 0xfc 0xfc 0xfc 0xfc 0xfc\n", | |
| " 0xfd 0xfd 0xfd 0xfd 0xfd 0xfd 0xfd 0xfd 0xfd 0xfd 0xfd 0xfd\n", | |
| " 0xfe 0xfe 0xfe 0xfe 0xfe 0xfe … 0xfe 0xfe 0xfe 0xfe 0xfe 0xfe\n", | |
| " 0xff 0xff 0xff 0xff 0xff 0xff 0xff 0xff 0xff 0xff 0xff 0xff\n", | |
| "\n", | |
| "...\n", | |
| "\n", | |
| "[:, :, 30] =\n", | |
| " 0x00 0x00 0x00 0x00 0x00 0x00 … 0x00 0x00 0x00 0x00 0x00 0x00\n", | |
| " 0x01 0x01 0x01 0x01 0x01 0x01 0x01 0x01 0x01 0x01 0x01 0x01\n", | |
| " 0x02 0x02 0x02 0x02 0x02 0x02 0x02 0x02 0x02 0x02 0x02 0x02\n", | |
| " 0x03 0x03 0x03 0x03 0x03 0x03 0x03 0x03 0x03 0x03 0x03 0x03\n", | |
| " 0x04 0x04 0x04 0x04 0x04 0x04 0x04 0x04 0x04 0x04 0x04 0x04\n", | |
| " 0x05 0x05 0x05 0x05 0x05 0x05 … 0x05 0x05 0x05 0x05 0x05 0x05\n", | |
| " 0x06 0x06 0x06 0x06 0x06 0x06 0x06 0x06 0x06 0x06 0x06 0x06\n", | |
| " 0x07 0x07 0x07 0x07 0x07 0x07 0x07 0x07 0x07 0x07 0x07 0x07\n", | |
| " 0x08 0x08 0x08 0x08 0x08 0x08 0x08 0x08 0x08 0x08 0x08 0x08\n", | |
| " 0x09 0x09 0x09 0x09 0x09 0x09 0x09 0x09 0x09 0x09 0x09 0x09\n", | |
| " 0x0a 0x0a 0x0a 0x0a 0x0a 0x0a … 0x0a 0x0a 0x0a 0x0a 0x0a 0x0a\n", | |
| " 0x0b 0x0b 0x0b 0x0b 0x0b 0x0b 0x0b 0x0b 0x0b 0x0b 0x0b 0x0b\n", | |
| " 0x0c 0x0c 0x0c 0x0c 0x0c 0x0c 0x0c 0x0c 0x0c 0x0c 0x0c 0x0c\n", | |
| " ⋮ ⋮ ⋱ ⋮ \n", | |
| " 0xf4 0xf4 0xf4 0xf4 0xf4 0xf4 … 0xf4 0xf4 0xf4 0xf4 0xf4 0xf4\n", | |
| " 0xf5 0xf5 0xf5 0xf5 0xf5 0xf5 0xf5 0xf5 0xf5 0xf5 0xf5 0xf5\n", | |
| " 0xf6 0xf6 0xf6 0xf6 0xf6 0xf6 0xf6 0xf6 0xf6 0xf6 0xf6 0xf6\n", | |
| " 0xf7 0xf7 0xf7 0xf7 0xf7 0xf7 0xf7 0xf7 0xf7 0xf7 0xf7 0xf7\n", | |
| " 0xf8 0xf8 0xf8 0xf8 0xf8 0xf8 0xf8 0xf8 0xf8 0xf8 0xf8 0xf8\n", | |
| " 0xf9 0xf9 0xf9 0xf9 0xf9 0xf9 … 0xf9 0xf9 0xf9 0xf9 0xf9 0xf9\n", | |
| " 0xfa 0xfa 0xfa 0xfa 0xfa 0xfa 0xfa 0xfa 0xfa 0xfa 0xfa 0xfa\n", | |
| " 0xfb 0xfb 0xfb 0xfb 0xfb 0xfb 0xfb 0xfb 0xfb 0xfb 0xfb 0xfb\n", | |
| " 0xfc 0xfc 0xfc 0xfc 0xfc 0xfc 0xfc 0xfc 0xfc 0xfc 0xfc 0xfc\n", | |
| " 0xfd 0xfd 0xfd 0xfd 0xfd 0xfd 0xfd 0xfd 0xfd 0xfd 0xfd 0xfd\n", | |
| " 0xfe 0xfe 0xfe 0xfe 0xfe 0xfe … 0xfe 0xfe 0xfe 0xfe 0xfe 0xfe\n", | |
| " 0xff 0xff 0xff 0xff 0xff 0xff 0xff 0xff 0xff 0xff 0xff 0xff\n", | |
| "\n", | |
| "[:, :, 31] =\n", | |
| " 0x00 0x00 0x00 0x00 0x00 0x00 … 0x00 0x00 0x00 0x00 0x00 0x00\n", | |
| " 0x01 0x01 0x01 0x01 0x01 0x01 0x01 0x01 0x01 0x01 0x01 0x01\n", | |
| " 0x02 0x02 0x02 0x02 0x02 0x02 0x02 0x02 0x02 0x02 0x02 0x02\n", | |
| " 0x03 0x03 0x03 0x03 0x03 0x03 0x03 0x03 0x03 0x03 0x03 0x03\n", | |
| " 0x04 0x04 0x04 0x04 0x04 0x04 0x04 0x04 0x04 0x04 0x04 0x04\n", | |
| " 0x05 0x05 0x05 0x05 0x05 0x05 … 0x05 0x05 0x05 0x05 0x05 0x05\n", | |
| " 0x06 0x06 0x06 0x06 0x06 0x06 0x06 0x06 0x06 0x06 0x06 0x06\n", | |
| " 0x07 0x07 0x07 0x07 0x07 0x07 0x07 0x07 0x07 0x07 0x07 0x07\n", | |
| " 0x08 0x08 0x08 0x08 0x08 0x08 0x08 0x08 0x08 0x08 0x08 0x08\n", | |
| " 0x09 0x09 0x09 0x09 0x09 0x09 0x09 0x09 0x09 0x09 0x09 0x09\n", | |
| " 0x0a 0x0a 0x0a 0x0a 0x0a 0x0a … 0x0a 0x0a 0x0a 0x0a 0x0a 0x0a\n", | |
| " 0x0b 0x0b 0x0b 0x0b 0x0b 0x0b 0x0b 0x0b 0x0b 0x0b 0x0b 0x0b\n", | |
| " 0x0c 0x0c 0x0c 0x0c 0x0c 0x0c 0x0c 0x0c 0x0c 0x0c 0x0c 0x0c\n", | |
| " ⋮ ⋮ ⋱ ⋮ \n", | |
| " 0xf4 0xf4 0xf4 0xf4 0xf4 0xf4 … 0xf4 0xf4 0xf4 0xf4 0xf4 0xf4\n", | |
| " 0xf5 0xf5 0xf5 0xf5 0xf5 0xf5 0xf5 0xf5 0xf5 0xf5 0xf5 0xf5\n", | |
| " 0xf6 0xf6 0xf6 0xf6 0xf6 0xf6 0xf6 0xf6 0xf6 0xf6 0xf6 0xf6\n", | |
| " 0xf7 0xf7 0xf7 0xf7 0xf7 0xf7 0xf7 0xf7 0xf7 0xf7 0xf7 0xf7\n", | |
| " 0xf8 0xf8 0xf8 0xf8 0xf8 0xf8 0xf8 0xf8 0xf8 0xf8 0xf8 0xf8\n", | |
| " 0xf9 0xf9 0xf9 0xf9 0xf9 0xf9 … 0xf9 0xf9 0xf9 0xf9 0xf9 0xf9\n", | |
| " 0xfa 0xfa 0xfa 0xfa 0xfa 0xfa 0xfa 0xfa 0xfa 0xfa 0xfa 0xfa\n", | |
| " 0xfb 0xfb 0xfb 0xfb 0xfb 0xfb 0xfb 0xfb 0xfb 0xfb 0xfb 0xfb\n", | |
| " 0xfc 0xfc 0xfc 0xfc 0xfc 0xfc 0xfc 0xfc 0xfc 0xfc 0xfc 0xfc\n", | |
| " 0xfd 0xfd 0xfd 0xfd 0xfd 0xfd 0xfd 0xfd 0xfd 0xfd 0xfd 0xfd\n", | |
| " 0xfe 0xfe 0xfe 0xfe 0xfe 0xfe … 0xfe 0xfe 0xfe 0xfe 0xfe 0xfe\n", | |
| " 0xff 0xff 0xff 0xff 0xff 0xff 0xff 0xff 0xff 0xff 0xff 0xff\n", | |
| "\n", | |
| "[:, :, 32] =\n", | |
| " 0x00 0x00 0x00 0x00 0x00 0x00 … 0x00 0x00 0x00 0x00 0x00 0x00\n", | |
| " 0x01 0x01 0x01 0x01 0x01 0x01 0x01 0x01 0x01 0x01 0x01 0x01\n", | |
| " 0x02 0x02 0x02 0x02 0x02 0x02 0x02 0x02 0x02 0x02 0x02 0x02\n", | |
| " 0x03 0x03 0x03 0x03 0x03 0x03 0x03 0x03 0x03 0x03 0x03 0x03\n", | |
| " 0x04 0x04 0x04 0x04 0x04 0x04 0x04 0x04 0x04 0x04 0x04 0x04\n", | |
| " 0x05 0x05 0x05 0x05 0x05 0x05 … 0x05 0x05 0x05 0x05 0x05 0x05\n", | |
| " 0x06 0x06 0x06 0x06 0x06 0x06 0x06 0x06 0x06 0x06 0x06 0x06\n", | |
| " 0x07 0x07 0x07 0x07 0x07 0x07 0x07 0x07 0x07 0x07 0x07 0x07\n", | |
| " 0x08 0x08 0x08 0x08 0x08 0x08 0x08 0x08 0x08 0x08 0x08 0x08\n", | |
| " 0x09 0x09 0x09 0x09 0x09 0x09 0x09 0x09 0x09 0x09 0x09 0x09\n", | |
| " 0x0a 0x0a 0x0a 0x0a 0x0a 0x0a … 0x0a 0x0a 0x0a 0x0a 0x0a 0x0a\n", | |
| " 0x0b 0x0b 0x0b 0x0b 0x0b 0x0b 0x0b 0x0b 0x0b 0x0b 0x0b 0x0b\n", | |
| " 0x0c 0x0c 0x0c 0x0c 0x0c 0x0c 0x0c 0x0c 0x0c 0x0c 0x0c 0x0c\n", | |
| " ⋮ ⋮ ⋱ ⋮ \n", | |
| " 0xf4 0xf4 0xf4 0xf4 0xf4 0xf4 … 0xf4 0xf4 0xf4 0xf4 0xf4 0xf4\n", | |
| " 0xf5 0xf5 0xf5 0xf5 0xf5 0xf5 0xf5 0xf5 0xf5 0xf5 0xf5 0xf5\n", | |
| " 0xf6 0xf6 0xf6 0xf6 0xf6 0xf6 0xf6 0xf6 0xf6 0xf6 0xf6 0xf6\n", | |
| " 0xf7 0xf7 0xf7 0xf7 0xf7 0xf7 0xf7 0xf7 0xf7 0xf7 0xf7 0xf7\n", | |
| " 0xf8 0xf8 0xf8 0xf8 0xf8 0xf8 0xf8 0xf8 0xf8 0xf8 0xf8 0xf8\n", | |
| " 0xf9 0xf9 0xf9 0xf9 0xf9 0xf9 … 0xf9 0xf9 0xf9 0xf9 0xf9 0xf9\n", | |
| " 0xfa 0xfa 0xfa 0xfa 0xfa 0xfa 0xfa 0xfa 0xfa 0xfa 0xfa 0xfa\n", | |
| " 0xfb 0xfb 0xfb 0xfb 0xfb 0xfb 0xfb 0xfb 0xfb 0xfb 0xfb 0xfb\n", | |
| " 0xfc 0xfc 0xfc 0xfc 0xfc 0xfc 0xfc 0xfc 0xfc 0xfc 0xfc 0xfc\n", | |
| " 0xfd 0xfd 0xfd 0xfd 0xfd 0xfd 0xfd 0xfd 0xfd 0xfd 0xfd 0xfd\n", | |
| " 0xfe 0xfe 0xfe 0xfe 0xfe 0xfe … 0xfe 0xfe 0xfe 0xfe 0xfe 0xfe\n", | |
| " 0xff 0xff 0xff 0xff 0xff 0xff 0xff 0xff 0xff 0xff 0xff 0xff" | |
| ] | |
| }, | |
| "execution_count": 14, | |
| "metadata": {}, | |
| "output_type": "execute_result" | |
| } | |
| ], | |
| "source": [ | |
| "read(d)" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 15, | |
| "id": "ongoing-genius", | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [ | |
| "name = zeros(Cchar, 64);\n", | |
| "HDF5.h5p_get_filter( HDF5.h5d_get_create_plist(d), 0, Ref{Cuint}(1), Ref{Csize_t}(0), Ref{Cuint}(), 64, pointer(name), Ref{Cuint}())" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 16, | |
| "id": "balanced-plenty", | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "data": { | |
| "text/plain": [ | |
| "\"HDF5 lz4 filter; see http://www.hdfgroup.org/services/contribut\"" | |
| ] | |
| }, | |
| "execution_count": 16, | |
| "metadata": {}, | |
| "output_type": "execute_result" | |
| } | |
| ], | |
| "source": [ | |
| "unsafe_string(pointer(name))" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 17, | |
| "id": "divided-burlington", | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "data": { | |
| "text/plain": [ | |
| "HDF5.ChunkStorage{IndexCartesian,3}\n", | |
| "Axes: (1:256:257, 1:256:257, 1:16:17)\n", | |
| "HDF5.Dataset: /DataSet/ResolutionLevel 0/TimePoint 0/Channel 0/Data (file: C:\\Users\\kittisopikulm\\.julia\\dev\\HDF5\\out_0.ims xfer_mode: 0)" | |
| ] | |
| }, | |
| "execution_count": 17, | |
| "metadata": {}, | |
| "output_type": "execute_result" | |
| } | |
| ], | |
| "source": [ | |
| "dcs = HDF5.ChunkStorage(d)" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 18, | |
| "id": "intermediate-prophet", | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "data": { | |
| "text/plain": [ | |
| "(0x00000000, UInt8[0x00, 0x00, 0x00, 0x00, 0x00, 0x10, 0x00, 0x00, 0x00, 0x10 … 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00])" | |
| ] | |
| }, | |
| "execution_count": 18, | |
| "metadata": {}, | |
| "output_type": "execute_result" | |
| } | |
| ], | |
| "source": [ | |
| "dcs[1,1,1]" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 19, | |
| "id": "norman-denial", | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "data": { | |
| "text/plain": [ | |
| "(1048576,)" | |
| ] | |
| }, | |
| "execution_count": 19, | |
| "metadata": {}, | |
| "output_type": "execute_result" | |
| } | |
| ], | |
| "source": [ | |
| "size(dcs[1,1,1][2])" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 20, | |
| "id": "wooden-ocean", | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "data": { | |
| "text/plain": [ | |
| "1048576" | |
| ] | |
| }, | |
| "execution_count": 20, | |
| "metadata": {}, | |
| "output_type": "execute_result" | |
| } | |
| ], | |
| "source": [ | |
| "uncompressed_block_size = reinterpret(Int64,reverse(dcs[1,1,1][2][1:8]))[1]" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 21, | |
| "id": "hundred-yellow", | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "data": { | |
| "text/plain": [ | |
| "4377" | |
| ] | |
| }, | |
| "execution_count": 21, | |
| "metadata": {}, | |
| "output_type": "execute_result" | |
| } | |
| ], | |
| "source": [ | |
| "block_size = reinterpret(Int32,reverse(dcs[1,1,1][2][13:16]))[1] " | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 22, | |
| "id": "basic-abortion", | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "data": { | |
| "text/plain": [ | |
| "4377-element Vector{UInt8}:\n", | |
| " 0xff\n", | |
| " 0xf1\n", | |
| " 0x00\n", | |
| " 0x01\n", | |
| " 0x02\n", | |
| " 0x03\n", | |
| " 0x04\n", | |
| " 0x05\n", | |
| " 0x06\n", | |
| " 0x07\n", | |
| " 0x08\n", | |
| " 0x09\n", | |
| " 0x0a\n", | |
| " ⋮\n", | |
| " 0xff\n", | |
| " 0xff\n", | |
| " 0xff\n", | |
| " 0xff\n", | |
| " 0xff\n", | |
| " 0xf6\n", | |
| " 0x50\n", | |
| " 0xfb\n", | |
| " 0xfc\n", | |
| " 0xfd\n", | |
| " 0xfe\n", | |
| " 0xff" | |
| ] | |
| }, | |
| "execution_count": 22, | |
| "metadata": {}, | |
| "output_type": "execute_result" | |
| } | |
| ], | |
| "source": [ | |
| "compressed_data = dcs[1,1,1][2][ (1:block_size) .+ 16 ]" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 23, | |
| "id": "bored-genealogy", | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [ | |
| "using CodecLz4" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 24, | |
| "id": "wound-screening", | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "data": { | |
| "text/plain": [ | |
| "1048576-element Vector{UInt8}:\n", | |
| " 0x00\n", | |
| " 0x01\n", | |
| " 0x02\n", | |
| " 0x03\n", | |
| " 0x04\n", | |
| " 0x05\n", | |
| " 0x06\n", | |
| " 0x07\n", | |
| " 0x08\n", | |
| " 0x09\n", | |
| " 0x0a\n", | |
| " 0x0b\n", | |
| " 0x0c\n", | |
| " ⋮\n", | |
| " 0xf4\n", | |
| " 0xf5\n", | |
| " 0xf6\n", | |
| " 0xf7\n", | |
| " 0xf8\n", | |
| " 0xf9\n", | |
| " 0xfa\n", | |
| " 0xfb\n", | |
| " 0xfc\n", | |
| " 0xfd\n", | |
| " 0xfe\n", | |
| " 0xff" | |
| ] | |
| }, | |
| "execution_count": 24, | |
| "metadata": {}, | |
| "output_type": "execute_result" | |
| } | |
| ], | |
| "source": [ | |
| "CodecLz4.lz4_decompress(compressed_data, uncompressed_block_size)" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 25, | |
| "id": "interracial-trash", | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [ | |
| "close(d)\n", | |
| "close(h5file)" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 26, | |
| "id": "suspected-interference", | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "data": { | |
| "text/plain": [ | |
| "\"C:\\\\Users\\\\kittisopikulm\\\\Documents\\\\eclipse-workspace\\\\dcimg4j\\\\_shuffle_lz4_no_downsample.ims\"" | |
| ] | |
| }, | |
| "execution_count": 26, | |
| "metadata": {}, | |
| "output_type": "execute_result" | |
| } | |
| ], | |
| "source": [ | |
| "# 16-bit \n", | |
| "imsfile2 = raw\"C:\\Users\\kittisopikulm\\Documents\\eclipse-workspace\\dcimg4j\\_shuffle_lz4_no_downsample.ims\"" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 27, | |
| "id": "developed-peter", | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "data": { | |
| "text/plain": [ | |
| "🔢 HDF5.Dataset: /DataSet/ResolutionLevel 0/TimePoint 2/Channel 0/Data (file: C:\\Users\\kittisopikulm\\Documents\\eclipse-workspace\\dcimg4j\\_shuffle_lz4_no_downsample.ims xfer_mode: 0)" | |
| ] | |
| }, | |
| "execution_count": 27, | |
| "metadata": {}, | |
| "output_type": "execute_result" | |
| } | |
| ], | |
| "source": [ | |
| "name = zeros(Cchar, 64);\n", | |
| "f2 = h5open(imsfile2)\n", | |
| "d2 = f2[\"DataSet\"][\"ResolutionLevel 0\"][\"TimePoint 2\"][\"Channel 0\"][\"Data\"]" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 28, | |
| "id": "female-force", | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "data": { | |
| "text/plain": [ | |
| "\"shuffle\"" | |
| ] | |
| }, | |
| "execution_count": 28, | |
| "metadata": {}, | |
| "output_type": "execute_result" | |
| } | |
| ], | |
| "source": [ | |
| "filter_idx = 0\n", | |
| "HDF5.h5p_get_filter( HDF5.h5d_get_create_plist(d2), filter_idx, Ref{Cuint}(1), Ref{Csize_t}(0), Ref{Cuint}(), 64, pointer(name), Ref{Cuint}())\n", | |
| "unsafe_string(pointer(name))" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 29, | |
| "id": "simplified-miracle", | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "data": { | |
| "text/plain": [ | |
| "\"HDF5 lz4 filter; see http://www.hdfgroup.org/services/contribut\"" | |
| ] | |
| }, | |
| "execution_count": 29, | |
| "metadata": {}, | |
| "output_type": "execute_result" | |
| } | |
| ], | |
| "source": [ | |
| "filter_idx = 1\n", | |
| "HDF5.h5p_get_filter( HDF5.h5d_get_create_plist(d2), filter_idx, Ref{Cuint}(1), Ref{Csize_t}(0), Ref{Cuint}(), 64, pointer(name), Ref{Cuint}())\n", | |
| "unsafe_string(pointer(name))" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 30, | |
| "id": "senior-celtic", | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [ | |
| "close(d2)\n", | |
| "close(f2)" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": null, | |
| "id": "valid-malta", | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [] | |
| } | |
| ], | |
| "metadata": { | |
| "kernelspec": { | |
| "display_name": "Julia 1.6.3 1.6.3", | |
| "language": "julia", | |
| "name": "julia-1.6.3-1.6" | |
| }, | |
| "language_info": { | |
| "file_extension": ".jl", | |
| "mimetype": "application/julia", | |
| "name": "julia", | |
| "version": "1.6.3" | |
| } | |
| }, | |
| "nbformat": 4, | |
| "nbformat_minor": 5 | |
| } |
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