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{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Data integration workflow of experimental campaign\n",
"\n",
"In this notebook, we will go through a our data integration workflow. This involves the following steps:\n",
"\n",
"1. Specify data integration file through YAML configuration file.\n",
"2. Create an integrated HDF5 file of experimental campaign from configuration file.\n",
"3. Display the created HDF5 file using a treemap\n",
"\n",
"## Import libraries and modules\n",
"\n",
"* Excecute (or Run) the Cell below"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Imports successful!\n"
]
}
],
"source": [
"from nbutils import add_project_path_to_sys_path\n",
"\n",
"# Add project root to sys.path\n",
"add_project_path_to_sys_path()\n",
"\n",
"try:\n",
" import src.hdf5_vis as hdf5_vis\n",
" import pipelines.data_integration as data_integration\n",
" print(\"Imports successful!\")\n",
"except ImportError as e:\n",
" print(f\"Import error: {e}\")"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Step 1: Specify data integration task through YAML configuration file\n",
"\n",
"* Create your configuration file (i.e., *.yaml file) adhering to the example yaml file in the input folder.\n",
"* Set up input directory and output directory paths and Excecute Cell.\n",
"\n"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [],
"source": [
"#output_filename_path = 'output_files/unified_file_smog_chamber_2024-04-07_UTC-OFST_+0200_NG.h5'\n",
"yaml_config_file_path = '../input_files/data_integr_config_file_TBR.yaml'\n",
"\n",
"#path_to_input_directory = 'output_files/kinetic_flowtube_study_2022-01-31_LuciaI'\n",
"#path_to_hdf5_file = hdf5_lib.create_hdf5_file_from_filesystem_path(path_to_input_directory)\n"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Step 2: Create an integrated HDF5 file of experimental campaign.\n",
"\n",
"* Excecute Cell. Here we run the function `integrate_data_sources` with input argument as the previously specified YAML config file."
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\n",
"[Start] Data integration :\n",
"Source: ..\\output_files\\collection_PSI_beamtime_ThorstenBR_2023-09-22_2023-09-25\n",
"Destination: ..\\output_files\\collection_PSI_beamtime_ThorstenBR_2023-09-22_2023-09-25.h5\n",
"\n",
"[Notice] The file '..\\output_files\\collection_PSI_beamtime_ThorstenBR_2023-09-22_2023-09-25.h5' already exists and will not be overwritten.\n",
"If you wish to replace it, please delete the existing file first and rerun the program.\n"
]
}
],
"source": [
"\n",
"hdf5_file_path = data_integration.run_pipeline(yaml_config_file_path)"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"['..\\\\output_files\\\\collection_PSI_beamtime_ThorstenBR_2023-09-22_2023-09-25.h5']"
]
},
"execution_count": 10,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"hdf5_file_path "
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Display integrated HDF5 file using a treemap\n",
"\n",
"* Excecute Cell. A visual representation in html format of the integrated file should be displayed and stored in the output directory folder"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"/NEXAFS\n",
"/NEXAFS/0001_20230922_155132_N_K_edge_Yanisha3.h5\n",
"/NEXAFS/0001_20230922_155132_N_K_edge_Yanisha3.h5/__DATA_TYPES__\n",
"/NEXAFS/0001_20230922_155132_N_K_edge_Yanisha3.h5/logs\n",
"/NEXAFS/0001_20230922_155132_N_K_edge_Yanisha3.h5/scan 1\n",
"/NEXAFS/0002_20230922_160137_N_K_edge_Yanisha3.h5\n",
"/NEXAFS/0002_20230922_160137_N_K_edge_Yanisha3.h5/__DATA_TYPES__\n",
"/NEXAFS/0002_20230922_160137_N_K_edge_Yanisha3.h5/logs\n",
"/NEXAFS/0002_20230922_160137_N_K_edge_Yanisha3.h5/scan 1\n",
"/NEXAFS/0002_20230922_160137_N_K_edge_Yanisha3.h5/scan 2\n",
"/NEXAFS/0002_20230922_160137_N_K_edge_Yanisha3.h5/scan 3\n",
"/NEXAFS/0002_20230922_160137_N_K_edge_Yanisha3.h5/scan 4\n",
"/NEXAFS/0002_20230922_160137_N_K_edge_Yanisha3.h5/scan 5\n",
"/NEXAFS/0048_20230922_075708_O_K_edge_Yang.h5\n",
"/NEXAFS/0048_20230922_075708_O_K_edge_Yang.h5/__DATA_TYPES__\n",
"/NEXAFS/0048_20230922_075708_O_K_edge_Yang.h5/logs\n",
"/NEXAFS/0048_20230922_075708_O_K_edge_Yang.h5/scan 1\n",
"/NEXAFS/0049_20230922_081328_O_K_edge_Yang.h5\n",
"/NEXAFS/0049_20230922_081328_O_K_edge_Yang.h5/__DATA_TYPES__\n",
"/NEXAFS/0049_20230922_081328_O_K_edge_Yang.h5/logs\n",
"/NEXAFS/0049_20230922_081328_O_K_edge_Yang.h5/scan 1\n",
"/NEXAFS/0050_20230922_082003_O_K_edge_Yang.h5\n",
"/NEXAFS/0050_20230922_082003_O_K_edge_Yang.h5/__DATA_TYPES__\n",
"/NEXAFS/0050_20230922_082003_O_K_edge_Yang.h5/logs\n",
"/NEXAFS/0050_20230922_082003_O_K_edge_Yang.h5/scan 1\n",
"/NEXAFS/0051_20230922_084410_O_K_edge_LL.h5\n",
"/NEXAFS/0051_20230922_084410_O_K_edge_LL.h5/__DATA_TYPES__\n",
"/NEXAFS/0051_20230922_084410_O_K_edge_LL.h5/logs\n",
"/NEXAFS/0051_20230922_084410_O_K_edge_LL.h5/scan 1\n",
"/NEXAFS/0052_20230922_085103_O_K_edge_LL.h5\n",
"/NEXAFS/0052_20230922_085103_O_K_edge_LL.h5/__DATA_TYPES__\n",
"/NEXAFS/0052_20230922_085103_O_K_edge_LL.h5/logs\n",
"/NEXAFS/0052_20230922_085103_O_K_edge_LL.h5/scan 1\n",
"/NEXAFS/0053_20230922_085154_O_K_edge_LL.h5\n",
"/NEXAFS/0053_20230922_085154_O_K_edge_LL.h5/__DATA_TYPES__\n",
"/NEXAFS/0053_20230922_085154_O_K_edge_LL.h5/logs\n",
"/NEXAFS/0053_20230922_085154_O_K_edge_LL.h5/scan 1\n",
"/NEXAFS/0054_20230922_090257_O_K_edge_LL.h5\n",
"/NEXAFS/0054_20230922_090257_O_K_edge_LL.h5/__DATA_TYPES__\n",
"/NEXAFS/0054_20230922_090257_O_K_edge_LL.h5/logs\n",
"/NEXAFS/0054_20230922_090257_O_K_edge_LL.h5/scan 1\n",
"/NEXAFS/0055_20230922_091352_N_K_edge_Yanisha3.h5\n",
"/NEXAFS/0055_20230922_091352_N_K_edge_Yanisha3.h5/__DATA_TYPES__\n",
"/NEXAFS/0055_20230922_091352_N_K_edge_Yanisha3.h5/logs\n",
"/NEXAFS/0055_20230922_091352_N_K_edge_Yanisha3.h5/scan 1\n",
"/Notes\n",
"/Pressure\n",
"/Pressure/2023-09-18_20.06.44_PC15490_NAPP_Chamber.dat\n",
"/Pressure/2023-09-22_10.17.46_PC15490_NAPP_Chamber.dat\n",
"/RGA\n",
"/RGA/RGA3.txt\n",
"/RGA/rga1.rga_Jun_24_2023_12-38-45_AM.txt\n",
"/RGA/rga1_Jun_21_2023_09-08-44_AM.txt\n",
"/SES\n",
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"<br><br>project: Beamtime May 2024, Ice Napp<br>experiment: beamtime<br>contact: ThorstenBR<br>level: 0",
"/NEXAFS",
"/NEXAFS/0001_20230922_155132_N_K_edge_Yanisha3.h5",
"/NEXAFS/0001_20230922_155132_N_K_edge_Yanisha3.h5/__DATA_TYPES__",
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"/NEXAFS/0001_20230922_155132_N_K_edge_Yanisha3.h5/scan 1",
"/NEXAFS/0002_20230922_160137_N_K_edge_Yanisha3.h5",
"/NEXAFS/0002_20230922_160137_N_K_edge_Yanisha3.h5/__DATA_TYPES__",
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"/NEXAFS/0002_20230922_160137_N_K_edge_Yanisha3.h5/scan 1",
"/NEXAFS/0002_20230922_160137_N_K_edge_Yanisha3.h5/scan 2",
"/NEXAFS/0002_20230922_160137_N_K_edge_Yanisha3.h5/scan 3",
"/NEXAFS/0002_20230922_160137_N_K_edge_Yanisha3.h5/scan 4",
"/NEXAFS/0002_20230922_160137_N_K_edge_Yanisha3.h5/scan 5",
"/NEXAFS/0048_20230922_075708_O_K_edge_Yang.h5",
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"/NEXAFS/0048_20230922_075708_O_K_edge_Yang.h5/scan 1",
"/NEXAFS/0049_20230922_081328_O_K_edge_Yang.h5",
"/NEXAFS/0049_20230922_081328_O_K_edge_Yang.h5/__DATA_TYPES__",
"/NEXAFS/0049_20230922_081328_O_K_edge_Yang.h5/logs",
"/NEXAFS/0049_20230922_081328_O_K_edge_Yang.h5/scan 1",
"/NEXAFS/0050_20230922_082003_O_K_edge_Yang.h5",
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"/NEXAFS/0051_20230922_084410_O_K_edge_LL.h5",
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"/NEXAFS/0051_20230922_084410_O_K_edge_LL.h5/scan 1",
"/NEXAFS/0052_20230922_085103_O_K_edge_LL.h5",
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"/NEXAFS/0052_20230922_085103_O_K_edge_LL.h5/scan 1",
"/NEXAFS/0053_20230922_085154_O_K_edge_LL.h5",
"/NEXAFS/0053_20230922_085154_O_K_edge_LL.h5/__DATA_TYPES__",
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"/NEXAFS/0053_20230922_085154_O_K_edge_LL.h5/scan 1",
"/NEXAFS/0054_20230922_090257_O_K_edge_LL.h5",
"/NEXAFS/0054_20230922_090257_O_K_edge_LL.h5/__DATA_TYPES__",
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"/NEXAFS/0055_20230922_091352_N_K_edge_Yanisha3.h5",
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"/Notes",
"/Pressure",
"/Pressure/2023-09-18_20.06.44_PC15490_NAPP_Chamber.dat",
"/Pressure/2023-09-18_20.06.44_PC15490_NAPP_Chamber.dat/data_table",
"/Pressure/2023-09-22_10.17.46_PC15490_NAPP_Chamber.dat",
"/Pressure/2023-09-22_10.17.46_PC15490_NAPP_Chamber.dat/data_table",
"/RGA",
"/RGA/RGA3.txt",
"/RGA/RGA3.txt/data_table",
"/RGA/RGA3.txt/table_preamble",
"/RGA/rga1.rga_Jun_24_2023_12-38-45_AM.txt",
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"/RGA/rga1.rga_Jun_24_2023_12-38-45_AM.txt/table_preamble",
"/RGA/rga1_Jun_21_2023_09-08-44_AM.txt",
"/RGA/rga1_Jun_21_2023_09-08-44_AM.txt/data_table",
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"colorbar": {
"outlinewidth": 0,
"ticks": ""
}
},
"colorscale": {
"diverging": [
[
0,
"#8e0152"
],
[
0.1,
"#c51b7d"
],
[
0.2,
"#de77ae"
],
[
0.3,
"#f1b6da"
],
[
0.4,
"#fde0ef"
],
[
0.5,
"#f7f7f7"
],
[
0.6,
"#e6f5d0"
],
[
0.7,
"#b8e186"
],
[
0.8,
"#7fbc41"
],
[
0.9,
"#4d9221"
],
[
1,
"#276419"
]
],
"sequential": [
[
0,
"#0d0887"
],
[
0.1111111111111111,
"#46039f"
],
[
0.2222222222222222,
"#7201a8"
],
[
0.3333333333333333,
"#9c179e"
],
[
0.4444444444444444,
"#bd3786"
],
[
0.5555555555555556,
"#d8576b"
],
[
0.6666666666666666,
"#ed7953"
],
[
0.7777777777777778,
"#fb9f3a"
],
[
0.8888888888888888,
"#fdca26"
],
[
1,
"#f0f921"
]
],
"sequentialminus": [
[
0,
"#0d0887"
],
[
0.1111111111111111,
"#46039f"
],
[
0.2222222222222222,
"#7201a8"
],
[
0.3333333333333333,
"#9c179e"
],
[
0.4444444444444444,
"#bd3786"
],
[
0.5555555555555556,
"#d8576b"
],
[
0.6666666666666666,
"#ed7953"
],
[
0.7777777777777778,
"#fb9f3a"
],
[
0.8888888888888888,
"#fdca26"
],
[
1,
"#f0f921"
]
]
},
"colorway": [
"#636efa",
"#EF553B",
"#00cc96",
"#ab63fa",
"#FFA15A",
"#19d3f3",
"#FF6692",
"#B6E880",
"#FF97FF",
"#FECB52"
],
"font": {
"color": "#2a3f5f"
},
"geo": {
"bgcolor": "white",
"lakecolor": "white",
"landcolor": "#E5ECF6",
"showlakes": true,
"showland": true,
"subunitcolor": "white"
},
"hoverlabel": {
"align": "left"
},
"hovermode": "closest",
"mapbox": {
"style": "light"
},
"paper_bgcolor": "white",
"plot_bgcolor": "#E5ECF6",
"polar": {
"angularaxis": {
"gridcolor": "white",
"linecolor": "white",
"ticks": ""
},
"bgcolor": "#E5ECF6",
"radialaxis": {
"gridcolor": "white",
"linecolor": "white",
"ticks": ""
}
},
"scene": {
"xaxis": {
"backgroundcolor": "#E5ECF6",
"gridcolor": "white",
"gridwidth": 2,
"linecolor": "white",
"showbackground": true,
"ticks": "",
"zerolinecolor": "white"
},
"yaxis": {
"backgroundcolor": "#E5ECF6",
"gridcolor": "white",
"gridwidth": 2,
"linecolor": "white",
"showbackground": true,
"ticks": "",
"zerolinecolor": "white"
},
"zaxis": {
"backgroundcolor": "#E5ECF6",
"gridcolor": "white",
"gridwidth": 2,
"linecolor": "white",
"showbackground": true,
"ticks": "",
"zerolinecolor": "white"
}
},
"shapedefaults": {
"line": {
"color": "#2a3f5f"
}
},
"ternary": {
"aaxis": {
"gridcolor": "white",
"linecolor": "white",
"ticks": ""
},
"baxis": {
"gridcolor": "white",
"linecolor": "white",
"ticks": ""
},
"bgcolor": "#E5ECF6",
"caxis": {
"gridcolor": "white",
"linecolor": "white",
"ticks": ""
}
},
"title": {
"x": 0.05
},
"xaxis": {
"automargin": true,
"gridcolor": "white",
"linecolor": "white",
"ticks": "",
"title": {
"standoff": 15
},
"zerolinecolor": "white",
"zerolinewidth": 2
},
"yaxis": {
"automargin": true,
"gridcolor": "white",
"linecolor": "white",
"ticks": "",
"title": {
"standoff": 15
},
"zerolinecolor": "white",
"zerolinewidth": 2
}
}
},
"width": 800
}
}
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"\n",
"if isinstance(hdf5_file_path ,list):\n",
" for path_item in hdf5_file_path :\n",
" hdf5_vis.display_group_hierarchy_on_a_treemap(path_item)\n",
"else:\n",
" hdf5_vis.display_group_hierarchy_on_a_treemap(hdf5_file_path)"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'output_files\\\\collection_PSI_beamtime_ThorstenBR_2023-09-22_2023-09-25.json'"
]
},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"import src.hdf5_ops as h5de \n",
"\n",
"h5de.serialize_metadata(hdf5_file_path[0],folder_depth=1,output_format='json')"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"['output_files\\\\collection_PSI_beamtime_ThorstenBR_2023-09-22_2023-09-25.h5']\n",
" dataset_name \\\n",
"0 NEXAFS/0001_20230922_155132_N_K_edge_Yanisha3.... \n",
"1 NEXAFS/0001_20230922_155132_N_K_edge_Yanisha3.... \n",
"2 NEXAFS/0001_20230922_155132_N_K_edge_Yanisha3.... \n",
"3 NEXAFS/0001_20230922_155132_N_K_edge_Yanisha3.... \n",
"4 NEXAFS/0001_20230922_155132_N_K_edge_Yanisha3.... \n",
"\n",
" parent_instrument parent_file \n",
"0 0001_20230922_155132_N_K_edge_Yanisha3.h5 logs \n",
"1 scan 1 attrs \n",
"2 scan 1 attrs \n",
"3 scan 1 attrs \n",
"4 scan 1 attrs \n"
]
}
],
"source": [
"import src.hdf5_ops as h5de \n",
"print(hdf5_file_path)\n",
"DataOpsAPI = h5de.HDF5DataOpsManager(hdf5_file_path[0])\n",
"\n",
"DataOpsAPI.load_file_obj()\n",
"\n",
"#DataOpsAPI.reformat_datetime_column('ICAD/HONO/2022_11_22_Channel1_Data.dat/data_table',\n",
"# 'Start Date/Time (UTC)',\n",
"# '%Y-%m-%d %H:%M:%S.%f', '%Y-%m-%d %H:%M:%S')\n",
"DataOpsAPI.extract_and_load_dataset_metadata()\n",
"df = DataOpsAPI.dataset_metadata_df\n",
"print(df.head())\n",
"\n",
"DataOpsAPI.unload_file_obj()\n",
"\n"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"DataOpsAPI.append_metadata('/',{'test_attr':'this is a test value'})\n",
"\n",
"DataOpsAPI.unload_file_obj()"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "multiphase_chemistry_env",
"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": "3.11.9"
}
},
"nbformat": 4,
"nbformat_minor": 4
}
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