From 7678d4223c60de334bb218461875ff186066ce9d Mon Sep 17 00:00:00 2001 From: rettigl Date: Sat, 27 Jul 2024 22:56:05 +0200 Subject: [PATCH 1/4] update definitions to work with multiformat mpes reader --- poetry.lock | 29 ++++++---- pyproject.toml | 4 +- specsscan/config/NXmpes_arpes_config.json | 69 +++++++++++------------ 3 files changed, 55 insertions(+), 47 deletions(-) diff --git a/poetry.lock b/poetry.lock index c4a3228..2b665ae 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2964,7 +2964,7 @@ files = [ anytree = "*" ase = ">=3.19.0" click = ">=7.1.2" -click-default-group = "*" +click_default_group = "*" h5py = ">=3.6.0" importlib-metadata = "*" lxml = ">=4.9.1" @@ -2987,25 +2987,34 @@ stm = ["pynxtools-stm"] xps = ["pynxtools-xps"] xrd = ["pynxtools-xrd"] +[package.source] +type = "git" +url = "https://github.com/FAIRmat-NFDI/pynxtools" +reference = "multi-format-reader" +resolved_reference = "1bd3e2d277119e8e10947b622cda6a2bbff5ec52" + [[package]] name = "pynxtools-mpes" -version = "0.1.1" +version = "0.1.2.dev33+gba416bc" description = "" optional = false python-versions = ">=3.8" -files = [ - {file = "pynxtools_mpes-0.1.1-py3-none-any.whl", hash = "sha256:44e5d1881d9e36cd5977831e4edf7cc96ef1dc595e0725119f255986cc5f658b"}, - {file = "pynxtools_mpes-0.1.1.tar.gz", hash = "sha256:e8f2eed853ebc7e28d24ba077994f6a3dd1848a3a3dcc7cbd1e115ff76ee7e46"}, -] +files = [] +develop = false [package.dependencies] h5py = ">=3.6.0" -pynxtools = ">=0.4.0" -PyYAML = ">=6.0" +pynxtools = {git = "https://github.com/FAIRmat-NFDI/pynxtools", rev = "multi-format-reader"} xarray = ">=0.20.2" [package.extras] -dev = ["mypy", "pip-tools", "pytest", "ruff (==0.3.4)", "types-pyyaml"] +dev = ["mypy", "pip-tools", "pytest", "ruff (==0.5.5)", "types-pyyaml"] + +[package.source] +type = "git" +url = "https://github.com/FAIRmat-NFDI/pynxtools-mpes.git" +reference = "updates-for-multiformat-reader" +resolved_reference = "ba416bc5dcdbaa83eab3c28c9f0c4f88969cb77b" [[package]] name = "pyparsing" @@ -4273,4 +4282,4 @@ notebook = ["ipykernel", "jupyter", "jupyterlab-h5web"] [metadata] lock-version = "2.0" python-versions = ">=3.8, <3.12" -content-hash = "6e2d6c6053c922d083f666a97534f43428aa46c8cdc413774277c2f20a8e4ef3" +content-hash = "378aeb12541715c9b575902e3b7b041e681ecb36ea0501bdaa97b1a8de2b6efa" diff --git a/pyproject.toml b/pyproject.toml index ff0a21d..20c8db3 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -26,8 +26,8 @@ ipywidgets = ">=7.7.1" matplotlib = ">=3.5.1" numpy = ">=1.21.6" opencv-python = ">=4.8.1.78" -pynxtools-mpes = ">=0.1.1" -pynxtools = ">=0.5.1" +pynxtools-mpes = { git = "https://github.com/FAIRmat-NFDI/pynxtools-mpes.git", branch = "updates-for-multiformat-reader" } +# pynxtools = { git = "https://github.com/FAIRmat-NFDI/pynxtools.git", branch = "multi-format-reader" } python-dateutil = ">=2.8.2" pyyaml = ">=6.0" xarray = ">=0.20.2" diff --git a/specsscan/config/NXmpes_arpes_config.json b/specsscan/config/NXmpes_arpes_config.json index d56f233..1719173 100755 --- a/specsscan/config/NXmpes_arpes_config.json +++ b/specsscan/config/NXmpes_arpes_config.json @@ -1,8 +1,7 @@ { "/@default": "entry", "/ENTRY[entry]/@default": "data", - "/ENTRY[entry]/definition": "NXmpes_arpes", - "/ENTRY[entry]/title": "@attrs:metadata/entry_title", + "/ENTRY[entry]/title": "['@eln:/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", "/ENTRY[entry]/experiment_facility": "Time Resolved ARPES", @@ -14,11 +13,11 @@ "/ENTRY[entry]/collection_time": "@attrs:metadata/timing/collection_time", "/ENTRY[entry]/collection_time/@units": "s", "/ENTRY[entry]/USER[user]": { - "name": "!@attrs:metadata/user0/name", - "role": "@attrs:metadata/user0/role", - "affiliation": "!@attrs:metadata/user0/affiliation", - "address": "@attrs:metadata/user0/address", - "email": "@attrs:metadata/user0/email" + "name": "!['@eln:/ENTRY/User/name', '@attrs:metadata/user0/name']", + "role": "['@eln:/ENTRY/User/role', '@attrs:metadata/user0/role']", + "affiliation": "!['@eln:/ENTRY/User/affiliation', '@attrs:metadata/user0/affiliation']", + "address": "['@eln:/ENTRY/User/address', '@attrs:metadata/user0/address']", + "email": "['@eln:/ENTRY/User/email', '@attrs:metadata/user0/email']" }, "/ENTRY[entry]/geometries/arpes_geometry": { "depends_on": "/entry/geometries/arpes_geometry/transformations/rot_y", @@ -34,7 +33,7 @@ "name": "Phoibos detector, at the endstation of the high rep-rate HHG source at FHI", "name/@short_name": "TR-ARPES @ FHI", "energy_resolution": { - "resolution": "@attrs:metadata/instrument/energy_resolution", + "resolution": "!['@eln:/ENTRY/Instrument/Analyzer/energy_resolution', '@attrs:metadata/instrument/energy_resolution']", "resolution/@units": "meV", "physical_quantity": "energy", "type": "estimated" @@ -54,7 +53,7 @@ "pressure_gauge": { "name": "sample_chamber_pressure", "measurement": "pressure", - "value": "@attrs:metadata/scan_info/trARPES:XGS600:PressureAC:P_RD", + "value": "!['@eln:/ENTRY/Sample/gas_pressure', '@attrs:metadata/scan_info/trARPES:XGS600:PressureAC:P_RD']", "value/@units": "mbar" } }, @@ -69,19 +68,19 @@ "fast_axes": "@attrs:metadata/scan_info/fast_axes", "slow_axes": "@attrs:metadata/scan_info/slow_axes", "energy_resolution": { - "resolution": "!@attrs:metadata/instrument/electronanalyser/energy_resolution", + "resolution": "!['@eln:/ENTRY/Instrument/Analyzer/energy_resolution', '@attrs:metadata/instrument/electronanalyser/energy_resolution']", "resolution/@units": "meV", "physical_quantity": "energy", "type": "derived" }, "angular_resolution": { - "resolution": "!@attrs:metadata/instrument/electronanalyser/angular_resolution", + "resolution": "!['@eln:/ENTRY/Instrument/Analyzer/angular_resolution', '@attrs:metadata/instrument/electronanalyser/angular_resolution']", "resolution/@units": "deg", "physical_quantity": "angle", "type": "derived" }, "spatial_resolution": { - "resolution": "!@attrs:metadata/instrument/electronanalyser/spatial_resolution", + "resolution": "!['@eln:/ENTRY/Instrument/Analyzer/spatial_resolution', '@attrs:metadata/instrument/electronanalyser/spatial_resolution']", "resolution/@units": "µm", "physical_quantity": "length", "type": "estimated" @@ -161,22 +160,22 @@ "probe": "photon", "type": "HHG laser", "mode": "Single Bunch", - "frequency": "@attrs:metadata/instrument/beam/probe/frequency", + "frequency": "['@eln:/ENTRY/Instrument/Source/Probe/frequency', '@attrs:metadata/instrument/beam/probe/frequency']", "frequency/@units": "kHz", "associated_beam": "/entry/instrument/beam_probe" }, "/ENTRY[entry]/INSTRUMENT[instrument]/beamTYPE[beam_probe]": { "distance": 0.0, "distance/@units": "mm", - "incident_energy": "!@attrs:metadata/instrument/beam/probe/incident_energy", + "incident_energy": "!['@eln:/ENTRY/Instrument/Beam/Probe/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": "['@eln:/ENTRY/Instrument/Beam/Probe/incident_energy_spread', '@attrs:metadata/instrument/beam/probe/incident_energy_spread']", "incident_energy_spread/@units": "eV", - "pulse_duration": "@attrs:metadata/instrument/beam/probe/pulse_duration", + "pulse_duration": "['@eln:/ENTRY/Instrument/Beam/Probe/pulse_duration', '@attrs:metadata/instrument/beam/probe/pulse_duration']", "pulse_duration/@units": "fs", - "incident_polarization": "@attrs:metadata/instrument/beam/probe/incident_polarization", + "incident_polarization": "['@eln:/ENTRY/Instrument/Beam/Probe/incident_polarization', '@attrs:metadata/instrument/beam/probe/incident_polarization']", "incident_polarization/@units": "V^2/mm^2", - "extent": "@attrs:metadata/instrument/beam/probe/extent", + "extent": "['@eln:/ENTRY/Instrument/Beam/Probe/extent', '@attrs:metadata/instrument/beam/probe/extent']", "extent/@units": "µm", "associated_source": "/entry/instrument/source_probe" }, @@ -185,30 +184,30 @@ "probe": "visible light", "type": "Optical Laser", "mode": "Single Bunch", - "frequency": "@attrs:metadata/instrument/beam/pump/frequency", + "frequency": "['@eln:/ENTRY/Instrument/Source/Pump/frequency', '@attrs:metadata/instrument/beam/pump/frequency']", "frequency/@units": "kHz", "associated_beam": "/entry/instrument/beam_pump" }, "/ENTRY[entry]/INSTRUMENT[instrument]/beamTYPE[beam_pump]": { "distance": 0.0, "distance/@units": "mm", - "incident_energy": "!@attrs:metadata/instrument/beam/pump/incident_energy", + "incident_energy": "!['@eln:/ENTRY/Instrument/Beam/Pump/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": "['@eln:/ENTRY/Instrument/Beam/Pump/incident_energy_spread', '@attrs:metadata/instrument/beam/pump/incident_energy_spread']", "incident_energy_spread/@units": "eV", - "incident_wavelength": "@attrs:metadata/instrument/beam/pump/incident_wavelength", + "incident_wavelength": "['@eln:/ENTRY/Instrument/Beam/Pump/incident_wavelength', '@attrs:metadata/instrument/beam/pump/incident_wavelength']", "incident_wavelength/@units": "nm", - "pulse_duration": "@attrs:metadata/instrument/beam/pump/pulse_duration", + "pulse_duration": "['@eln:/ENTRY/Instrument/Beam/Pump/pulse_duration', '@attrs:metadata/instrument/beam/pump/pulse_duration']", "pulse_duration/@units": "fs", - "incident_polarization": "@attrs:metadata/instrument/beam/pump/incident_polarization", + "incident_polarization": "['@eln:/ENTRY/Instrument/Beam/Pump/incident_polarization', '@attrs:metadata/instrument/beam/pump/incident_polarization']", "incident_polarization/@units": "V^2/mm^2", - "pulse_energy": "@attrs:metadata/instrument/beam/pump/pulse_energy", + "pulse_energy": "['@eln:/ENTRY/Instrument/Beam/Pump/pulse_energy', '@attrs:metadata/instrument/beam/pump/pulse_energy']", "pulse_energy/@units": "µJ", - "average_power": "@attrs:metadata/instrument/beam/pump/average_power", + "average_power": "['@eln:/ENTRY/Instrument/Beam/Pump/average_power', '@attrs:metadata/instrument/beam/pump/average_power']", "average_power/@units": "mW", - "extent": "@attrs:metadata/instrument/beam/pump/extent", + "extent": "['@eln:/ENTRY/Instrument/Beam/Pump/extent', '@attrs:metadata/instrument/beam/pump/extent']", "extent/@units": "µm", - "fluence": "@attrs:metadata/instrument/beam/pump/fluence", + "fluence": "['@eln:/ENTRY/Instrument/Beam/Pump/fluence', '@attrs:metadata/instrument/beam/pump/fluence']", "fluence/@units": "mJ/cm^2", "associated_source": "/entry/instrument/source_pump" }, @@ -216,7 +215,7 @@ "temperature_sensor": { "name": "sample_temperature", "measurement": "temperature", - "value": "!@attrs:metadata/scan_info/trARPES:Carving:TEMP_RBV", + "value": "!['@eln:/ENTRY/Instrument/Manipulator/sample_temperature', '@attrs:metadata/scan_info/trARPES:Carving:TEMP_RBV']", "value/@units": "K" }, "sample_bias_voltmeter": { @@ -228,7 +227,7 @@ "drain_current_amperemeter": { "name": "drain_current", "measurement": "current", - "value": "!@attrs:metadata/scan_info/trARPES:Sample:Measure", + "value": "!['@eln:/ENTRY/Instrument/Manipulator/drain_current', '@attrs:metadata/scan_info/trARPES:Sample:Measure']", "value/@units": "A" }, "depends_on": "/entry/instrument/manipulator/transformations/trans_z", @@ -251,12 +250,12 @@ } }, "/ENTRY[entry]/SAMPLE[sample]": { - "preparation_date": "@attrs:metadata/sample/preparation_date", - "history/notes/description": "@attrs:metadata/sample/sample_history", - "description": "@attrs:metadata/sample/chemical_formula", - "name": "@attrs:metadata/sample/name", + "preparation_date": "['@eln:/ENTRY/Sample/preparation_date', '@attrs:metadata/sample/preparation_date']", + "history/notes/description": "['@eln:/ENTRY/Sample/sample_history', '@attrs:metadata/sample/sample_history']", + "description": "['@eln:/ENTRY/Sample/description', '@attrs:metadata/sample/chemical_formula']", + "name": "!['@eln:/ENTRY/Sample/name', '@attrs:metadata/sample/name']", "situation": "vacuum", - "SUBSTANCE[substance]/molecular_formula_hill": "@attrs:metadata/sample/chemical_formula", + "SUBSTANCE[substance]/molecular_formula_hill": "['@eln:/ENTRY/Sample/chemical_formula', '@attrs:metadata/sample/chemical_formula']", "temperature_env": { "temperature_sensor": "@link:/entry/instrument/manipulator/temperature_sensor" }, From 47533b5a8e449c22623c2454b84e0d9274381d9d Mon Sep 17 00:00:00 2001 From: rettigl Date: Sat, 27 Jul 2024 23:30:09 +0200 Subject: [PATCH 2/4] update lockfile --- poetry.lock | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/poetry.lock b/poetry.lock index 2b665ae..4ec28ae 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2991,7 +2991,7 @@ xrd = ["pynxtools-xrd"] type = "git" url = "https://github.com/FAIRmat-NFDI/pynxtools" reference = "multi-format-reader" -resolved_reference = "1bd3e2d277119e8e10947b622cda6a2bbff5ec52" +resolved_reference = "2e61d8e2858c7067edd6f7c60f955080077c76bc" [[package]] name = "pynxtools-mpes" @@ -3014,7 +3014,7 @@ dev = ["mypy", "pip-tools", "pytest", "ruff (==0.5.5)", "types-pyyaml"] type = "git" url = "https://github.com/FAIRmat-NFDI/pynxtools-mpes.git" reference = "updates-for-multiformat-reader" -resolved_reference = "ba416bc5dcdbaa83eab3c28c9f0c4f88969cb77b" +resolved_reference = "dee73d2c5f83f5f9148e1bdc218fac8170145432" [[package]] name = "pyparsing" From b8bdb97602df56e4123a2c5dec585a0cf2577f72 Mon Sep 17 00:00:00 2001 From: rettigl Date: Wed, 14 Aug 2024 13:55:24 +0200 Subject: [PATCH 3/4] update pynxtools and pynxtools-mpes --- poetry.lock | 58 +++++++++++++++++++++----------------------------- pyproject.toml | 4 ++-- 2 files changed, 26 insertions(+), 36 deletions(-) diff --git a/poetry.lock b/poetry.lock index 4ec28ae..e4b2129 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2326,13 +2326,13 @@ test = ["pep440", "pre-commit", "pytest", "testpath"] [[package]] name = "nbsphinx" -version = "0.9.4" +version = "0.9.5" description = "Jupyter Notebook Tools for Sphinx" optional = false python-versions = ">=3.6" files = [ - {file = "nbsphinx-0.9.4-py3-none-any.whl", hash = "sha256:22cb1d974a8300e8118ca71aea1f649553743c0c5830a54129dcd446e6a8ba17"}, - {file = "nbsphinx-0.9.4.tar.gz", hash = "sha256:042a60806fc23d519bc5bef59d95570713913fe442fda759d53e3aaf62104794"}, + {file = "nbsphinx-0.9.5-py3-none-any.whl", hash = "sha256:d82f71084425db1f48e72515f15c25b4de8652ceaab513ee462ac05f1b8eae0a"}, + {file = "nbsphinx-0.9.5.tar.gz", hash = "sha256:736916e7b0dab28fc904f4a9ae3b53a9a50c29fccc6329c052fcc7485abcf2b7"}, ] [package.dependencies] @@ -2951,20 +2951,20 @@ windows-terminal = ["colorama (>=0.4.6)"] [[package]] name = "pynxtools" -version = "0.5.2" +version = "0.6.0" description = "Extend NeXus for experiments and characterization in Materials Science and Materials Engineering and serve as a NOMAD parser implementation for NeXus." optional = false python-versions = ">=3.8" files = [ - {file = "pynxtools-0.5.2-py3-none-any.whl", hash = "sha256:4d9abb366cf05a7fc85e1789de523b4836dac1c02031e94ac6de82d64c7d72f3"}, - {file = "pynxtools-0.5.2.tar.gz", hash = "sha256:717d11d0ff0e3ad07bce26fe4d2014fe48725fee3b0f77cf98ebc5e83acbfbb7"}, + {file = "pynxtools-0.6.0-py3-none-any.whl", hash = "sha256:75ee95196244ae3234480a16d7e9248049b23548ade69a6658d7fbb128529e6f"}, + {file = "pynxtools-0.6.0.tar.gz", hash = "sha256:ebb394507d0580aeb447767f295027921a4336476cce359a5afa5a604a3d91c2"}, ] [package.dependencies] anytree = "*" ase = ">=3.19.0" click = ">=7.1.2" -click_default_group = "*" +click-default-group = "*" h5py = ">=3.6.0" importlib-metadata = "*" lxml = ">=4.9.1" @@ -2987,35 +2987,25 @@ stm = ["pynxtools-stm"] xps = ["pynxtools-xps"] xrd = ["pynxtools-xrd"] -[package.source] -type = "git" -url = "https://github.com/FAIRmat-NFDI/pynxtools" -reference = "multi-format-reader" -resolved_reference = "2e61d8e2858c7067edd6f7c60f955080077c76bc" - [[package]] name = "pynxtools-mpes" -version = "0.1.2.dev33+gba416bc" +version = "0.2.0" description = "" optional = false python-versions = ">=3.8" -files = [] -develop = false +files = [ + {file = "pynxtools_mpes-0.2.0-py3-none-any.whl", hash = "sha256:eca6182d08e66236fcb56d23efaf0e6a689f6480f3d44997f67193b01e9a6ccb"}, + {file = "pynxtools_mpes-0.2.0.tar.gz", hash = "sha256:3dddc3c71949baab4d836573a51cfb08fbc6401c696d2bb770131542c5c6a9a7"}, +] [package.dependencies] h5py = ">=3.6.0" -pynxtools = {git = "https://github.com/FAIRmat-NFDI/pynxtools", rev = "multi-format-reader"} +pynxtools = ">=0.6.0" xarray = ">=0.20.2" [package.extras] dev = ["mypy", "pip-tools", "pytest", "ruff (==0.5.5)", "types-pyyaml"] -[package.source] -type = "git" -url = "https://github.com/FAIRmat-NFDI/pynxtools-mpes.git" -reference = "updates-for-multiformat-reader" -resolved_reference = "dee73d2c5f83f5f9148e1bdc218fac8170145432" - [[package]] name = "pyparsing" version = "3.1.2" @@ -3678,18 +3668,18 @@ win32 = ["pywin32"] [[package]] name = "setuptools" -version = "72.1.0" +version = "72.2.0" description = "Easily download, build, install, upgrade, and uninstall Python packages" optional = true python-versions = ">=3.8" files = [ - {file = "setuptools-72.1.0-py3-none-any.whl", hash = "sha256:5a03e1860cf56bb6ef48ce186b0e557fdba433237481a9a625176c2831be15d1"}, - {file = "setuptools-72.1.0.tar.gz", hash = "sha256:8d243eff56d095e5817f796ede6ae32941278f542e0f941867cc05ae52b162ec"}, + {file = "setuptools-72.2.0-py3-none-any.whl", hash = "sha256:f11dd94b7bae3a156a95ec151f24e4637fb4fa19c878e4d191bfb8b2d82728c4"}, + {file = "setuptools-72.2.0.tar.gz", hash = "sha256:80aacbf633704e9c8bfa1d99fa5dd4dc59573efcf9e4042c13d3bcef91ac2ef9"}, ] [package.extras] core = ["importlib-metadata (>=6)", "importlib-resources (>=5.10.2)", "jaraco.text (>=3.7)", "more-itertools (>=8.8)", "ordered-set (>=3.1.1)", "packaging (>=24)", "platformdirs (>=2.6.2)", "tomli (>=2.0.1)", "wheel (>=0.43.0)"] -doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "pyproject-hooks (!=1.1)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (>=1,<2)", "sphinx-reredirects", "sphinxcontrib-towncrier"] +doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "pyproject-hooks (!=1.1)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (>=1,<2)", "sphinx-reredirects", "sphinxcontrib-towncrier", "towncrier (<24.7)"] test = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "importlib-metadata", "ini2toml[lite] (>=0.14)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "jaraco.test", "mypy (==1.11.*)", "packaging (>=23.2)", "pip (>=19.1)", "pyproject-hooks (!=1.1)", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-home (>=0.5)", "pytest-mypy", "pytest-perf", "pytest-ruff (<0.4)", "pytest-ruff (>=0.2.1)", "pytest-ruff (>=0.3.2)", "pytest-subprocess", "pytest-timeout", "pytest-xdist (>=3)", "tomli", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"] [[package]] @@ -3727,13 +3717,13 @@ files = [ [[package]] name = "soupsieve" -version = "2.5" +version = "2.6" description = "A modern CSS selector implementation for Beautiful Soup." optional = false python-versions = ">=3.8" files = [ - {file = "soupsieve-2.5-py3-none-any.whl", hash = "sha256:eaa337ff55a1579b6549dc679565eac1e3d000563bcb1c8ab0d0fefbc0c2cdc7"}, - {file = "soupsieve-2.5.tar.gz", hash = "sha256:5663d5a7b3bfaeee0bc4372e7fc48f9cff4940b3eec54a6451cc5299f1097690"}, + {file = "soupsieve-2.6-py3-none-any.whl", hash = "sha256:e72c4ff06e4fb6e4b5a9f0f55fe6e81514581fca1515028625d0f299c602ccc9"}, + {file = "soupsieve-2.6.tar.gz", hash = "sha256:e2e68417777af359ec65daac1057404a3c8a5455bb8abc36f1a9866ab1a51abb"}, ] [[package]] @@ -4000,13 +3990,13 @@ files = [ [[package]] name = "tomlkit" -version = "0.13.0" +version = "0.13.2" description = "Style preserving TOML library" optional = false python-versions = ">=3.8" files = [ - {file = "tomlkit-0.13.0-py3-none-any.whl", hash = "sha256:7075d3042d03b80f603482d69bf0c8f345c2b30e41699fd8883227f89972b264"}, - {file = "tomlkit-0.13.0.tar.gz", hash = "sha256:08ad192699734149f5b97b45f1f18dad7eb1b6d16bc72ad0c2335772650d7b72"}, + {file = "tomlkit-0.13.2-py3-none-any.whl", hash = "sha256:7a974427f6e119197f670fbbbeae7bef749a6c14e793db934baefc1b5f03efde"}, + {file = "tomlkit-0.13.2.tar.gz", hash = "sha256:fff5fe59a87295b278abd31bec92c15d9bc4a06885ab12bcea52c71119392e79"}, ] [[package]] @@ -4282,4 +4272,4 @@ notebook = ["ipykernel", "jupyter", "jupyterlab-h5web"] [metadata] lock-version = "2.0" python-versions = ">=3.8, <3.12" -content-hash = "378aeb12541715c9b575902e3b7b041e681ecb36ea0501bdaa97b1a8de2b6efa" +content-hash = "4b8e575739c922aa344ea4946ab363e07b4c266a211630420f68d50a751bb2d7" diff --git a/pyproject.toml b/pyproject.toml index 20c8db3..1e93a96 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -26,8 +26,8 @@ ipywidgets = ">=7.7.1" matplotlib = ">=3.5.1" numpy = ">=1.21.6" opencv-python = ">=4.8.1.78" -pynxtools-mpes = { git = "https://github.com/FAIRmat-NFDI/pynxtools-mpes.git", branch = "updates-for-multiformat-reader" } -# pynxtools = { git = "https://github.com/FAIRmat-NFDI/pynxtools.git", branch = "multi-format-reader" } +pynxtools-mpes = "^0.2.0" +pynxtools = "^0.6.0" python-dateutil = ">=2.8.2" pyyaml = ">=6.0" xarray = ">=0.20.2" From ade26acfcf957f4fc53ec8c322f2b650591375a5 Mon Sep 17 00:00:00 2001 From: rettigl Date: Wed, 14 Aug 2024 13:57:15 +0200 Subject: [PATCH 4/4] use flexible entry name --- specsscan/config/NXmpes_arpes_config.json | 56 +++++++++++------------ 1 file changed, 28 insertions(+), 28 deletions(-) diff --git a/specsscan/config/NXmpes_arpes_config.json b/specsscan/config/NXmpes_arpes_config.json index 1719173..464fe44 100755 --- a/specsscan/config/NXmpes_arpes_config.json +++ b/specsscan/config/NXmpes_arpes_config.json @@ -1,25 +1,25 @@ { "/@default": "entry", - "/ENTRY[entry]/@default": "data", - "/ENTRY[entry]/title": "['@eln:/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", - "/ENTRY[entry]/experiment_facility": "Time Resolved ARPES", - "/ENTRY[entry]/experiment_laboratory": "Clean Room 4", - "/ENTRY[entry]/entry_identifier": "@attrs:metadata/loader/scan_path", - "/ENTRY[entry]/end_time": "@attrs:metadata/timing/acquisition_stop", - "/ENTRY[entry]/duration": "@attrs:metadata/timing/acquisition_duration", - "/ENTRY[entry]/duration/@units": "s", - "/ENTRY[entry]/collection_time": "@attrs:metadata/timing/collection_time", - "/ENTRY[entry]/collection_time/@units": "s", - "/ENTRY[entry]/USER[user]": { + "/ENTRY/@default": "data", + "/ENTRY/title": "['@eln:/ENTRY/title', '@attrs:metadata/entry_title']", + "/ENTRY/start_time": "@attrs:metadata/timing/acquisition_start", + "/ENTRY/experiment_institution": "Fritz Haber Institute - Max Planck Society", + "/ENTRY/experiment_facility": "Time Resolved ARPES", + "/ENTRY/experiment_laboratory": "Clean Room 4", + "/ENTRY/entry_identifier": "@attrs:metadata/loader/scan_path", + "/ENTRY/end_time": "@attrs:metadata/timing/acquisition_stop", + "/ENTRY/duration": "@attrs:metadata/timing/acquisition_duration", + "/ENTRY/duration/@units": "s", + "/ENTRY/collection_time": "@attrs:metadata/timing/collection_time", + "/ENTRY/collection_time/@units": "s", + "/ENTRY/USER[user]": { "name": "!['@eln:/ENTRY/User/name', '@attrs:metadata/user0/name']", "role": "['@eln:/ENTRY/User/role', '@attrs:metadata/user0/role']", "affiliation": "!['@eln:/ENTRY/User/affiliation', '@attrs:metadata/user0/affiliation']", "address": "['@eln:/ENTRY/User/address', '@attrs:metadata/user0/address']", "email": "['@eln:/ENTRY/User/email', '@attrs:metadata/user0/email']" }, - "/ENTRY[entry]/geometries/arpes_geometry": { + "/ENTRY/geometries/arpes_geometry": { "depends_on": "/entry/geometries/arpes_geometry/transformations/rot_y", "TRANSFORMATIONS[transformations]": { "AXISNAME[rot_y]/@depends_on": ".", @@ -29,7 +29,7 @@ "AXISNAME[rot_y]/@vector": [0, 1, 0] } }, - "/ENTRY[entry]/INSTRUMENT[instrument]": { + "/ENTRY/INSTRUMENT[instrument]": { "name": "Phoibos detector, at the endstation of the high rep-rate HHG source at FHI", "name/@short_name": "TR-ARPES @ FHI", "energy_resolution": { @@ -57,7 +57,7 @@ "value/@units": "mbar" } }, - "/ENTRY[entry]/INSTRUMENT[instrument]/ELECTRONANALYSER[electronanalyser]": { + "/ENTRY/INSTRUMENT[instrument]/ELECTRONANALYSER[electronanalyser]": { "description": "SPECS Phoibos 150 Hemispherical Energy Analyzer", "device_information": { "vendor": "SPECS GmbH", @@ -116,14 +116,14 @@ "AXISNAME[rot_y]/@vector": [0, 1, 0] } }, - "/ENTRY[entry]/INSTRUMENT[instrument]/ELECTRONANALYSER[electronanalyser]/COLLECTIONCOLUMN[collectioncolumn]": { + "/ENTRY/INSTRUMENT[instrument]/ELECTRONANALYSER[electronanalyser]/COLLECTIONCOLUMN[collectioncolumn]": { "projection": "@attrs:metadata/scan_info/projection", "scheme": "@attrs:metadata/scan_info/scheme", "lens_mode": "@attrs:metadata/scan_info/LensMode", "working_distance": 40.0, "working_distance/@units": "mm" }, - "/ENTRY[entry]/INSTRUMENT[instrument]/ELECTRONANALYSER[electronanalyser]/ENERGYDISPERSION[energydispersion]": { + "/ENTRY/INSTRUMENT[instrument]/ELECTRONANALYSER[electronanalyser]/ENERGYDISPERSION[energydispersion]": { "energy_scan_mode": "@attrs:metadata/scan_info/energy_scan_mode", "pass_energy": "@attrs:metadata/scan_info/PassEnergy", "pass_energy/@units": "eV", @@ -141,7 +141,7 @@ "shape": "grid" } }, - "/ENTRY[entry]/INSTRUMENT[instrument]/ELECTRONANALYSER[electronanalyser]/DETECTOR[detector]": { + "/ENTRY/INSTRUMENT[instrument]/ELECTRONANALYSER[electronanalyser]/DETECTOR[detector]": { "amplifier_type": "MCP", "detector_type": "Phosphor+CCD", "sensor_pixels": [ @@ -155,7 +155,7 @@ "detector_voltage": "@attrs:metadata/scan_info/ScreenVoltage", "detector_voltage/@units": "V" }, - "/ENTRY[entry]/INSTRUMENT[instrument]/sourceTYPE[source_probe]": { + "/ENTRY/INSTRUMENT[instrument]/sourceTYPE[source_probe]": { "name": "HHG @ TR-ARPES @ FHI", "probe": "photon", "type": "HHG laser", @@ -164,7 +164,7 @@ "frequency/@units": "kHz", "associated_beam": "/entry/instrument/beam_probe" }, - "/ENTRY[entry]/INSTRUMENT[instrument]/beamTYPE[beam_probe]": { + "/ENTRY/INSTRUMENT[instrument]/beamTYPE[beam_probe]": { "distance": 0.0, "distance/@units": "mm", "incident_energy": "!['@eln:/ENTRY/Instrument/Beam/Probe/incident_energy', '@attrs:metadata/instrument/beam/probe/incident_energy']", @@ -179,7 +179,7 @@ "extent/@units": "µm", "associated_source": "/entry/instrument/source_probe" }, - "/ENTRY[entry]/INSTRUMENT[instrument]/sourceTYPE[source_pump]": { + "/ENTRY/INSTRUMENT[instrument]/sourceTYPE[source_pump]": { "name": "OPCPA @ TR-ARPES @ FHI", "probe": "visible light", "type": "Optical Laser", @@ -188,7 +188,7 @@ "frequency/@units": "kHz", "associated_beam": "/entry/instrument/beam_pump" }, - "/ENTRY[entry]/INSTRUMENT[instrument]/beamTYPE[beam_pump]": { + "/ENTRY/INSTRUMENT[instrument]/beamTYPE[beam_pump]": { "distance": 0.0, "distance/@units": "mm", "incident_energy": "!['@eln:/ENTRY/Instrument/Beam/Pump/incident_energy', '@attrs:metadata/instrument/beam/pump/incident_energy']", @@ -211,7 +211,7 @@ "fluence/@units": "mJ/cm^2", "associated_source": "/entry/instrument/source_pump" }, - "/ENTRY[entry]/INSTRUMENT[instrument]/MANIPULATOR[manipulator]": { + "/ENTRY/INSTRUMENT[instrument]/MANIPULATOR[manipulator]": { "temperature_sensor": { "name": "sample_temperature", "measurement": "temperature", @@ -249,7 +249,7 @@ "AXISNAME[rot_x]/@vector": [1, 0, 0] } }, - "/ENTRY[entry]/SAMPLE[sample]": { + "/ENTRY/SAMPLE[sample]": { "preparation_date": "['@eln:/ENTRY/Sample/preparation_date', '@attrs:metadata/sample/preparation_date']", "history/notes/description": "['@eln:/ENTRY/Sample/sample_history', '@attrs:metadata/sample/sample_history']", "description": "['@eln:/ENTRY/Sample/description', '@attrs:metadata/sample/chemical_formula']", @@ -327,13 +327,13 @@ "AXISNAME[trans_x]/@vector": [0, 1, 0] } }, - "/ENTRY[entry]/PROCESS[process]/CALIBRATION[energy_calibration]":{ + "/ENTRY/PROCESS[process]/CALIBRATION[energy_calibration]":{ "calibrated_axis": "@link:/entry/data/energy" }, - "/ENTRY[entry]/PROCESS[process]/CALIBRATION[angular0_calibration]":{ + "/ENTRY/PROCESS[process]/CALIBRATION[angular0_calibration]":{ "calibrated_axis": "@link:/entry/data/angular0" }, - "/ENTRY[entry]/data": { + "/ENTRY/data": { "@axes": "@data:dims", "@*_indices": "@data:*.index", "@signal": "data",