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[package.dependencies] @@ -4994,4 +4980,4 @@ notebook = ["ipykernel", "jupyter", "jupyterlab", "jupyterlab-h5web"] [metadata] lock-version = "2.0" python-versions = ">=3.9, <3.12.3, !=3.11.9" -content-hash = "f8b41a3e994c5b654366626a57e5a71c522829cb188d60c97a2d7ad2937a67ad" +content-hash = "0d4830168219b4ad9cc4787d1f432fd1975f2bad131963d0f83017a63fb36d0e" diff --git a/pyproject.toml b/pyproject.toml index 4e0189d2..3d0a7424 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -3,7 +3,7 @@ name = "sed-processor" packages = [ {include = "sed"} ] -version = "0.1.10a6" +version = "0.1.10a8" description = "Single Event Data Frame Processor: Backend to handle photoelectron resolved datastreams" authors = ["OpenCOMPES team "] readme = "README.md" @@ -27,18 +27,17 @@ numba = ">=0.55.1" numpy = ">=1.18, <2.0" pandas = ">=1.4.1" psutil = ">=5.9.0" -pynxtools-mpes = ">=0.0.3" -pynxtools = ">=0.3.1" +pynxtools-mpes = ">=0.1.1" +pynxtools = ">=0.5.0" pyyaml = ">=6.0.0" scipy = ">=1.8.0" -setuptools = ">70" symmetrize = ">=0.5.5" threadpoolctl = ">=3.1.0" tifffile = ">=2022.2.9" tqdm = ">=4.62.3" xarray = ">=0.20.2" joblib = ">=1.2.0" -pyarrow = ">=14.0.1" +pyarrow = ">=14.0.1, <17.0" jupyter = {version = ">=1.0.0", optional = true} ipykernel = {version = ">=6.9.1", optional = true} jupyterlab = {version = "^3.4.0", optional = true} diff --git a/sed/config/NXmpes_config.json b/sed/config/NXmpes_config.json index a636ef62..33f512c3 100755 --- a/sed/config/NXmpes_config.json +++ b/sed/config/NXmpes_config.json @@ -2,7 +2,6 @@ "/@default": "entry", "/ENTRY[entry]/@default": "data", "/ENTRY[entry]/definition": "NXmpes", - "/ENTRY[entry]/definition/@version": "None", "/ENTRY[entry]/title": "@attrs:metadata/entry_title", "/ENTRY[entry]/start_time": "@attrs:metadata/timing/acquisition_start", "/ENTRY[entry]/experiment_institution": "Fritz Haber Institute - Max Planck Society", @@ -15,9 +14,9 @@ "/ENTRY[entry]/collection_time": "@attrs:metadata/timing/collection_time", "/ENTRY[entry]/collection_time/@units": "s", "/ENTRY[entry]/USER[user]": { - "name": "@attrs:metadata/user0/name", + "name": "!@attrs:metadata/user0/name", "role": "@attrs:metadata/user0/role", - "affiliation": "@attrs:metadata/user0/affiliation", + "affiliation": "!@attrs:metadata/user0/affiliation", "address": "@attrs:metadata/user0/address", "email": "@attrs:metadata/user0/email" }, @@ -45,7 +44,7 @@ "pressure_gauge": { "name": "sample_chamber_pressure", "measurement": "pressure", - "value": "@attrs:metadata/file/trARPES:XGS600:PressureAC:P_RD", + "value": "!@attrs:metadata/file/trARPES:XGS600:PressureAC:P_RD", "value/@units": "mbar" } }, @@ -63,19 +62,19 @@ ], "slow_axes": "@attrs:metadata/instrument/analyzer/slow_axes", "energy_resolution": { - "resolution": "@attrs:metadata/instrument/analyzer/energy_resolution", + "resolution": "!@attrs:metadata/instrument/analyzer/energy_resolution", "resolution/@units": "meV", "physical_quantity": "energy", "type": "estimated" }, "momentum_resolution": { - "resolution": "@attrs:metadata/instrument/analyzer/momentum_resolution", + "resolution": "!@attrs:metadata/instrument/analyzer/momentum_resolution", "resolution/@units": "1/angstrom", "physical_quantity": "momentum", "type": "estimated" }, "spatial_resolution": { - "resolution": "@attrs:metadata/instrument/analyzer/spatial_resolution", + "resolution": "!@attrs:metadata/instrument/analyzer/spatial_resolution", "resolution/@units": "µm", "physical_quantity": "length", "type": "estimated" @@ -173,7 +172,7 @@ "/ENTRY[entry]/INSTRUMENT[instrument]/beamTYPE[beam_probe]": { "distance": 0.0, "distance/@units": "mm", - "incident_energy": "@attrs:metadata/instrument/beam/probe/incident_energy", + "incident_energy": "!@attrs:metadata/instrument/beam/probe/incident_energy", "incident_energy/@units": "eV", "incident_energy_spread": "@attrs:metadata/instrument/beam/probe/incident_energy_spread", "incident_energy_spread/@units": "eV", @@ -197,7 +196,7 @@ "/ENTRY[entry]/INSTRUMENT[instrument]/beamTYPE[beam_pump]": { "distance": 0.0, "distance/@units": "mm", - "incident_energy": "@attrs:metadata/instrument/beam/pump/incident_energy", + "incident_energy": "!@attrs:metadata/instrument/beam/pump/incident_energy", "incident_energy/@units": "eV", "incident_energy_spread": "@attrs:metadata/instrument/beam/pump/incident_energy_spread", "incident_energy_spread/@units": "eV", @@ -221,13 +220,13 @@ "temperature_sensor": { "name": "sample_temperature", "measurement": "temperature", - "value": "@attrs:metadata/file/trARPES:Carving:TEMP_RBV", + "value": "!@attrs:metadata/file/trARPES:Carving:TEMP_RBV", "value/@units": "K" }, "sample_bias_voltmeter": { "name": "sample_bias", "measurement": "voltage", - "value": "@attrs:metadata/file/KTOF:Lens:Sample:V", + "value": "!@attrs:metadata/file/KTOF:Lens:Sample:V", "value/@units": "V" }, "depends_on": "/entry/instrument/manipulator/transformations/trans_z", diff --git a/sed/config/flash_example_config.yaml b/sed/config/flash_example_config.yaml index d9ce9184..ceaffe42 100644 --- a/sed/config/flash_example_config.yaml +++ b/sed/config/flash_example_config.yaml @@ -8,7 +8,7 @@ core: # the beamline where experiment took place beamline: pg2 # the ID number of the beamtime - beamtime_id: 11013410 + beamtime_id: 11019101 # the year of the beamtime year: 2023 # the instrument used @@ -18,9 +18,9 @@ core: # provided, the loader will try to find the data based on year beamtimeID etc paths: # location of the raw data. - data_raw_dir: "tests/data/loader/flash/" + data_raw_dir: "" # location of the intermediate parquet files. - data_parquet_dir: "tests/data/loader/flash/parquet" + data_parquet_dir: "" binning: # Histogram computation mode to use. diff --git a/tests/test_processor.py b/tests/test_processor.py index 42e583b2..a52bf959 100644 --- a/tests/test_processor.py +++ b/tests/test_processor.py @@ -5,6 +5,7 @@ import csv import glob import itertools +import logging import os import tempfile from importlib.util import find_spec @@ -15,6 +16,8 @@ import numpy as np import pytest import xarray as xr +import yaml +from pynxtools.dataconverter.convert import ValidationFailed from sed import SedProcessor from sed.core.config import parse_config @@ -1017,7 +1020,7 @@ def test_get_normalization_histogram() -> None: metadata["sample"]["name"] = "Sample Name" -def test_save() -> None: +def test_save(caplog) -> None: """Test the save functionality""" config = parse_config( config={"dataframe": {"tof_binning": 1}}, @@ -1025,6 +1028,11 @@ def test_save() -> None: user_config=package_dir + "/../sed/config/mpes_example_config.yaml", system_config={}, ) + config["metadata"]["lens_mode_config"]["6kV_kmodem4.0_30VTOF_453ns_focus.sav"][ + "MCPfront" + ] = 21.0 + config["metadata"]["lens_mode_config"]["6kV_kmodem4.0_30VTOF_453ns_focus.sav"]["Z1"] = 2450 + config["metadata"]["lens_mode_config"]["6kV_kmodem4.0_30VTOF_453ns_focus.sav"]["F"] = 69.23 processor = SedProcessor( folder=df_folder, config=config, @@ -1052,9 +1060,41 @@ def test_save() -> None: processor.save("output.h5") assert os.path.isfile("output.h5") os.remove("output.h5") + # convert using the fail=True keyword. This ensures that the pynxtools backend will throw + # and error if any validation problems occur. processor.save( "output.nxs", input_files=df_folder + "../../../../sed/config/NXmpes_config.json", + fail=True, ) assert os.path.isfile("output.nxs") + # Test that a validation error is raised if a required field is missing + del processor.binned.attrs["metadata"]["sample"]["name"] + with pytest.raises(ValidationFailed): + processor.save( + "result.nxs", + input_files=df_folder + "../../../../sed/config/NXmpes_config.json", + fail=True, + ) + # Check that the issues are raised as warnings per default: + caplog.clear() + with open("temp_eln.yaml", "w") as f: + yaml.dump({"Instrument": {"undocumented_field": "undocumented entry"}}, f) + with caplog.at_level(logging.WARNING): + processor.save( + "result.nxs", + input_files=[df_folder + "../../../../sed/config/NXmpes_config.json"], + eln_data="temp_eln.yaml", + ) + assert ( + caplog.messages[0] + == "The data entry corresponding to /ENTRY[entry]/SAMPLE[sample]/name is required and " + "hasn't been supplied by the reader." + ) + assert ( + caplog.messages[1] + == "Field /ENTRY[entry]/INSTRUMENT[instrument]/undocumented_field written without " + "documentation." + ) os.remove("output.nxs") + os.remove("temp_eln.yaml") diff --git a/tutorial/4_hextof_workflow.ipynb b/tutorial/4_hextof_workflow.ipynb index a2804a40..4de9c825 100644 --- a/tutorial/4_hextof_workflow.ipynb +++ b/tutorial/4_hextof_workflow.ipynb @@ -47,7 +47,16 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "### Download and unpack data" + "### Get data paths" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "The paths are such that if you are on Maxwell, it uses those. Otherwise data is downloaded in current directory from Zenodo.\n", + "\n", + "Generally, if it is your beamtime, you can both read the raw data and write to processed directory. However, for the public data, you can not write to processed directory." ] }, { @@ -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 = \"Gd_W110/processed/\"\n", + "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/\"" ] }, { @@ -99,35 +113,13 @@ "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": {}, @@ -766,7 +758,7 @@ " 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", " preserve_mean=True # preserve the mean of the delay axis\n", ")" ] @@ -967,7 +959,7 @@ ], "metadata": { "kernelspec": { - "display_name": "python3", + "display_name": "Python 3.9", "language": "python", "name": "python3" }, @@ -985,5 +977,5 @@ } }, "nbformat": 4, - "nbformat_minor": 2 + "nbformat_minor": 4 }