{ "cells": [ { "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ "# Import supporting package" ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [], "source": [ "import xarray as xr\n", "import numpy as np\n", "\n", "import matplotlib.pyplot as plt\n", "\n", "from DataContainer.ReadData import read_hdf5_file\n", "from Analyser.ImagingAnalyser import ImageAnalyser\n", "from Analyser.FitAnalyser import FitAnalyser\n", "\n", "imageAnalyser = ImageAnalyser()" ] }, { "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ "## Start a client for parallel computing" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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Client

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Client-1a44c769-ea9b-11ed-88cc-80e82ce2fa8e

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Connection method: Cluster objectCluster type: distributed.LocalCluster
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Cluster Info

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LocalCluster

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b16f0063

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Status: runningUsing processes: True
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Scheduler Info

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Scheduler

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Scheduler-8571d7e2-e6e5-4263-a9ed-50018e90379b

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\n", " Comm: tcp://127.0.0.1:55356\n", " \n", " Workers: 6\n", "
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Workers

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Worker: 0

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\n", " Comm: tcp://127.0.0.1:55387\n", " \n", " Total threads: 10\n", "
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Worker: 1

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Worker: 2

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Worker: 3

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Worker: 4

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Worker: 5

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" ], "text/plain": [ "" ] }, "execution_count": 2, "metadata": {}, "output_type": "execute_result" } ], "source": [ "from dask.distributed import Client\n", "client = Client(n_workers=6, threads_per_worker=10, processes=True, memory_limit='10GB')\n", "client" ] }, { "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ "# Read data" ] }, { "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ "## Set file path" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [], "source": [ "# filepath = \"//DyLabNAS/Data/Evaporative_Cooling/2023/05/03/0043/*.h5\"\n", "# filepath = \"//DyLabNAS/Data/Evaporative_Cooling/2023/04/18/0003/2023-04-18_0003_Evaporative_Cooling_000.h5\"\n", "\n", "filepath = \"//DyLabNAS/Data/Repetition_scan/2023/04/21/0002/*.h5\"\n", "\n", "# filepath = r\"./testData/0000/*.h5\"\n", "\n", "# filepath = \"//DyLabNAS/Data/Evaporative_Cooling/2023/04/18/0003/*.h5\"" ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [], "source": [ "groupList = [\n", " \"images/MOT_3D_Camera/in_situ_absorption\",\n", " # \"images/ODT_1_Axis_Camera/in_situ_absorption\",\n", "]\n", "\n", "dskey = {\n", " \"images/MOT_3D_Camera/in_situ_absorption\": \"camera_1\",\n", " # \"images/ODT_1_Axis_Camera/in_situ_absorption\": \"camera_2\",\n", "}\n", "\n", "dataSetDict = {\n", " dskey[groupList[i]]: read_hdf5_file(filepath, groupList[i])\n", " for i in range(len(groupList))\n", "}" ] }, { "cell_type": "code", "execution_count": 37, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Today's date: 2023-05-04\n", "d3 = 23/05/04\n", "True\n" ] } ], "source": [ "from datetime import date\n", "\n", "today = date.today()\n", "print(\"Today's date:\", today)\n", "\n", "d3 = today.strftime(\"%y/%m/%d\")\n", "print(\"d3 =\", d3)\n", "print(isinstance(d3, str))" ] }, { "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ "## Rechunk the data for parallel computing" ] }, { "cell_type": "code", "execution_count": 5, "metadata": {}, "outputs": [], "source": [ "dataSet = dataSetDict[\"camera_1\"]\n", "\n", "scanAxis = dataSet.scanAxis\n", "\n", "# dataSet = dataSet.chunk(\n", "# {\n", "# # \"compZ_current_sg\": \"auto\",\n", "# \"sin_mod_freq\": \"auto\",\n", "# \"runs\": 2,\n", "# \"x\": \"auto\",\n", "# \"y\": \"auto\",\n", "# }\n", "# )" ] }, { "cell_type": "code", "execution_count": 27, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "final_amp\n", "runs\n", "x\n", "y\n" ] } ], "source": [ "for key in dataset.dims.keys():\n", " print(key)" ] }, { "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ "# Calculate absorption imaging" ] }, { "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ "## get OD images" ] }, { "cell_type": "code", "execution_count": 13, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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<xarray.Dataset>\n",
       "Dimensions:     (final_amp: 11, runs: 3, x: 1200, y: 1920)\n",
       "Coordinates:\n",
       "  * final_amp   (final_amp) float64 3e-05 5.5e-05 8e-05 ... 0.000255 0.00028\n",
       "  * runs        (runs) float64 0.0 1.0 2.0\n",
       "Dimensions without coordinates: x, y\n",
       "Data variables:\n",
       "    atoms       (final_amp, runs, x, y) uint16 dask.array<chunksize=(1, 1, 1200, 1920), meta=np.ndarray>\n",
       "    background  (final_amp, runs, x, y) uint16 dask.array<chunksize=(1, 1, 1200, 1920), meta=np.ndarray>\n",
       "    dark        (final_amp, runs, x, y) uint16 dask.array<chunksize=(1, 1, 1200, 1920), meta=np.ndarray>\n",
       "    shotNum     (final_amp, runs) <U2 '00' '11' '22' '01' ... '10' '21' '32'\n",
       "    OD          (final_amp, runs, x, y) float64 dask.array<chunksize=(1, 1, 1200, 1920), meta=np.ndarray>\n",
       "Attributes: (12/96)\n",
       "    TOF_free:                          0.01\n",
       "    abs_img_freq:                      110.858\n",
       "    absorption_imaging_flag:           True\n",
       "    backup_data:                       True\n",
       "    blink_off_time:                    nan\n",
       "    blink_on_time:                     nan\n",
       "    ...                                ...\n",
       "    z_offset:                          0.189\n",
       "    z_offset_img:                      0.189\n",
       "    final_amp:                         [3.00e-05 5.50e-05 8.00e-05 1.05e-04 1...\n",
       "    runs:                              [0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 1. 1...\n",
       "    scanAxis:                          ['final_amp', 'runs']\n",
       "    scanAxisLength:                    [33. 33.]
" ], "text/plain": [ "\n", "Dimensions: (final_amp: 11, runs: 3, x: 1200, y: 1920)\n", "Coordinates:\n", " * final_amp (final_amp) float64 3e-05 5.5e-05 8e-05 ... 0.000255 0.00028\n", " * runs (runs) float64 0.0 1.0 2.0\n", "Dimensions without coordinates: x, y\n", "Data variables:\n", " atoms (final_amp, runs, x, y) uint16 dask.array\n", " background (final_amp, runs, x, y) uint16 dask.array\n", " dark (final_amp, runs, x, y) uint16 dask.array\n", " shotNum (final_amp, runs) \n", "Attributes: (12/96)\n", " TOF_free: 0.01\n", " abs_img_freq: 110.858\n", " absorption_imaging_flag: True\n", " backup_data: True\n", " blink_off_time: nan\n", " blink_on_time: nan\n", " ... ...\n", " z_offset: 0.189\n", " z_offset_img: 0.189\n", " final_amp: [3.00e-05 5.50e-05 8.00e-05 1.05e-04 1...\n", " runs: [0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 1. 1...\n", " scanAxis: ['final_amp', 'runs']\n", " scanAxisLength: [33. 33.]" ] }, "execution_count": 13, "metadata": {}, "output_type": "execute_result" } ], "source": [ "dataSet = imageAnalyser.get_absorption_images(dataSet)\n", "\n", "dataSet" ] }, { "cell_type": "code", "execution_count": 18, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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<xarray.Dataset>\n",
       "Dimensions:     (final_amp: 11, runs: 3, x: 1200, y: 1920)\n",
       "Coordinates:\n",
       "  * final_amp   (final_amp) float64 3e-05 5.5e-05 8e-05 ... 0.000255 0.00028\n",
       "  * runs        (runs) float64 0.0 1.0 2.0\n",
       "Dimensions without coordinates: x, y\n",
       "Data variables:\n",
       "    atoms       (final_amp, runs, x, y) uint16 98 101 109 106 ... 146 140 140\n",
       "    background  (final_amp, runs, x, y) uint16 99 101 113 103 ... 147 137 137\n",
       "    dark        (final_amp, runs, x, y) uint16 50 51 51 50 50 ... 50 51 50 49 49\n",
       "    shotNum     (final_amp, runs) <U2 '00' '11' '22' '01' ... '10' '21' '32'\n",
       "    OD          (final_amp, runs, x, y) float64 nan nan ... -0.03352 -0.03352\n",
       "Attributes: (12/96)\n",
       "    TOF_free:                          0.01\n",
       "    abs_img_freq:                      110.858\n",
       "    absorption_imaging_flag:           True\n",
       "    backup_data:                       True\n",
       "    blink_off_time:                    nan\n",
       "    blink_on_time:                     nan\n",
       "    ...                                ...\n",
       "    z_offset:                          0.189\n",
       "    z_offset_img:                      0.189\n",
       "    final_amp:                         [3.00e-05 5.50e-05 8.00e-05 1.05e-04 1...\n",
       "    runs:                              [0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 1. 1...\n",
       "    scanAxis:                          ['final_amp', 'runs']\n",
       "    scanAxisLength:                    [33. 33.]
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