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Update hextof tutorial notebook #421

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merged 5 commits into from
Jul 8, 2024
Merged

Update hextof tutorial notebook #421

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2e36c15
update hextof notebook
zain-sohail Jun 19, 2024
23ef8d0
update hextof notebook
zain-sohail Jun 19, 2024
9a69e4d
make buffer path local to user
zain-sohail Jun 20, 2024
f30870d
remove the cal file
zain-sohail Jul 8, 2024
30bd0f2
Merge remote-tracking branch 'origin/main' into update-hextof-tutorial
rettigl Jul 8, 2024
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95 changes: 34 additions & 61 deletions tutorial/4_hextof_workflow.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -47,7 +47,16 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"### Download and unpack data"
"### Get data paths"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"If it is your beamtime, you can access both read the raw data and write to processed directory. For the public data, you can not write to processed directory.\n",
"\n",
"The paths are such that if you are on Maxwell, it uses those. Otherwise data is downloaded in current directory from Zenodo."
]
},
{
Expand All @@ -56,10 +65,15 @@
"metadata": {},
"outputs": [],
"source": [
"# data_path can be defined and used to store the data in a specific location\n",
"dataset.get(\"Gd_W110\") # Put in Path to a storage of at least 10 Gbyte free space.\n",
"path = dataset.dir\n",
"print(path)"
"beamtime_dir = \"/asap3/flash/gpfs/pg2/2023/data/11019101\" # on Maxwell\n",
"if os.path.exists(beamtime_dir) and os.access(beamtime_dir, os.R_OK):\n",
" path = beamtime_dir + \"/raw/hdf/offline/fl1user3\"\n",
" buffer_path = beamtime_dir + \"/processed/tutorial/\"\n",
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"else:\n",
" # data_path can be defined and used to store the data in a specific location\n",
" dataset.get(\"Gd_W110\") # Put in Path to a storage of at least 10 Gbyte free space.\n",
" path = dataset.dir\n",
" buffer_path = path + \"/processed/\""
]
},
{
Expand All @@ -84,6 +98,8 @@
},
"outputs": [],
"source": [
"# file to store the calibration parameters in\n",
"cal_file = \"hextof_tutorial_cal.yaml\" \n",
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"# pick the default configuration file for hextof@FLASH\n",
"config_file = Path('../sed/config/flash_example_config.yaml')\n",
"assert config_file.exists()"
Expand All @@ -99,58 +115,13 @@
"config_override = {\n",
" \"core\": {\n",
" \"paths\": {\n",
" \"data_raw_dir\": \"\",\n",
" \"data_parquet_dir\": \"\"\n",
" \"data_raw_dir\": path,\n",
" \"data_parquet_dir\": buffer_path\n",
" },\n",
" },\n",
"}"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"If it is your beamtime, you can access both read the raw data and write to processed directory. For the public data, you can not write to processed directory."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"config_override['core']['paths']['data_raw_dir'] = \"/asap3/flash/gpfs/pg2/2023/data/11019101/raw/hdf/offline/fl1user3\"\n",
"# If this will not work for you, please change it to a path where you have write access\n",
"config_override['core']['paths']['data_parquet_dir'] = \"/asap3/flash/gpfs/pg2/2023/data/11019101/processed\"\n",
"# So we write to user space\n",
"config_override['core']['paths']['data_parquet_dir'] = path + \"/processed\"\n",
"# If you aren't using maxwell and downloaded the data, use this path\n",
"config_override['core']['paths']['data_raw_dir'] = path"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### cleanup previous config files\n",
"In this notebook, we will show how calibration parameters can be generated. Therefore we want to clean the local directory of previously generated files.\n",
"\n",
"**WARNING** running the cell below will delete the \"sed_config.yaml\" file in the local directory. If these contain precious calibration parameters, **DO NOT RUN THIS CELL**."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"local_folder_config = Path('./sed_config.yaml')\n",
"if local_folder_config.exists():\n",
" os.remove(local_folder_config)\n",
" print(f'deleted local config file {local_folder_config}')\n",
"assert not local_folder_config.exists()"
]
},
{
"cell_type": "markdown",
"metadata": {},
Expand All @@ -175,7 +146,7 @@
"metadata": {},
"outputs": [],
"source": [
"sp = SedProcessor(runs=[44762], config=config_override, system_config=config_file, collect_metadata=False, force_recreate=True)\n",
"sp = SedProcessor(runs=[44762], config=config_override, system_config=config_file, collect_metadata=False)\n",
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"# You can set collect_metadata=True if the scicat_url and scicat_token are defined"
]
},
Expand Down Expand Up @@ -330,7 +301,7 @@
"metadata": {},
"outputs": [],
"source": [
"fig,ax = plt.subplots(1,3,figsize=(8,2), layout='tight')\n",
"fig,ax = plt.subplots(1,3,figsize=(10,3), layout='tight')\n",
"res_chessy.plot(ax=ax[0], robust=True)\n",
"res_t05.plot(ax=ax[1], robust=True)\n",
"res_t10.plot(ax=ax[2], robust=True)"
Expand Down Expand Up @@ -648,8 +619,8 @@
"metadata": {},
"outputs": [],
"source": [
"sp.save_energy_calibration()\n",
"sp.save_energy_offset()"
"sp.save_energy_calibration(cal_file)\n",
"sp.save_energy_offset(cal_file)"
]
},
{
Expand All @@ -665,7 +636,7 @@
"metadata": {},
"outputs": [],
"source": [
"sp.save_workflow_params()"
"sp.save_workflow_params(cal_file)"
]
},
{
Expand All @@ -692,6 +663,7 @@
"sp = SedProcessor(\n",
" runs=[44824,44825,44826,44827],\n",
" config=config_override,\n",
" user_config=cal_file,\n",
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" system_config=config_file,\n",
" collect_metadata=False,\n",
")"
Expand Down Expand Up @@ -767,7 +739,7 @@
" constant=-1463.7, # this is time zero\n",
" flip_delay_axis=True, # invert the direction of the delay axis\n",
" columns=['bam'], # use the bam to offset the values\n",
" weights=[0.001], # bam is in fs, delay in ps\n",
" weights=[-0.001], # bam is in fs, delay in ps\n",
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" preserve_mean=True # preserve the mean of the delay axis\n",
")"
]
Expand Down Expand Up @@ -860,7 +832,7 @@
},
"outputs": [],
"source": [
"sp.save_delay_offsets()"
"sp.save_delay_offsets(cal_file)"
]
},
{
Expand All @@ -884,6 +856,7 @@
"sp = SedProcessor(\n",
" runs=[44824,44825,44826,44827],\n",
" config=config_override,\n",
" user_config=cal_file,\n",
" system_config=config_file,\n",
" collect_metadata=False\n",
")"
Expand Down Expand Up @@ -982,9 +955,9 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.6"
"version": "3.8.12"
}
},
"nbformat": 4,
"nbformat_minor": 2
"nbformat_minor": 4
}