From 9b34836848c612c0ca1dd738434a864fcbf28127 Mon Sep 17 00:00:00 2001 From: rettigl Date: Mon, 20 May 2024 01:57:51 +0000 Subject: [PATCH 1/2] Update dependencies --- poetry.lock | 511 +++++++++++++++++++++++++++++++++------------------- 1 file changed, 330 insertions(+), 181 deletions(-) diff --git a/poetry.lock b/poetry.lock index 19973a9..a7f032f 100644 --- a/poetry.lock +++ b/poetry.lock @@ -16,6 +16,25 @@ type = "legacy" url = "https://pypi.org/simple" reference = "pypi-public" +[[package]] +name = "annotated-types" +version = "0.6.0" +description = "Reusable constraint types to use with typing.Annotated" +optional = false +python-versions = ">=3.8" +files = [ + {file = "annotated_types-0.6.0-py3-none-any.whl", hash = "sha256:0641064de18ba7a25dee8f96403ebc39113d0cb953a01429249d5c7564666a43"}, + {file = "annotated_types-0.6.0.tar.gz", hash = "sha256:563339e807e53ffd9c267e99fc6d9ea23eb8443c08f112651963e24e22f84a5d"}, +] + +[package.dependencies] +typing-extensions = {version = 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"transformations": { + "TRANSFORMATIONS[transformations]": { "AXISNAME[trans_z]/@depends_on": "analyzer_elevation", "AXISNAME[trans_z]": 40.0, "AXISNAME[trans_z]/@transformation_type": "translation", @@ -116,7 +116,6 @@ "AXISNAME[rot_y]/@transformation_type": "rotation", "AXISNAME[rot_y]/@units": "degrees", "AXISNAME[rot_y]/@vector": [0, 1, 0] - } }, "/ENTRY[entry]/INSTRUMENT[instrument]/ELECTRONANALYSER[electronanalyser]/COLLECTIONCOLUMN[collectioncolumn]": { @@ -130,8 +129,8 @@ "energy_scan_mode": "@attrs:metadata/scan_info/energy_scan_mode", "pass_energy": "@attrs:metadata/scan_info/PassEnergy", "pass_energy/@units": "eV", - "kinetic_energy": "@attrs:metadata/scan_info/KineticEnergy", - "kinetic_energy/@units": "eV", + "center_energy": "@attrs:metadata/scan_info/KineticEnergy", + "center_energy/@units": "eV", "scheme": "hemispherical", "diameter": 300.0, "diameter/@units": "mm", @@ -158,7 +157,7 @@ "detector_voltage": "@attrs:metadata/scan_info/ScreenVoltage", "detector_voltage/@units": "V" }, - "/ENTRY[entry]/INSTRUMENT[instrument]/source_TYPE[source_probe]": { + "/ENTRY[entry]/INSTRUMENT[instrument]/sourceTYPE[source_probe]": { "name": "HHG @ TR-ARPES @ FHI", "probe": "photon", "type": "HHG laser", @@ -167,7 +166,7 @@ "frequency/@units": "kHz", "associated_beam": "/entry/instrument/beam_probe" }, - "/ENTRY[entry]/INSTRUMENT[instrument]/beam_TYPE[beam_probe]": { + "/ENTRY[entry]/INSTRUMENT[instrument]/beamTYPE[beam_probe]": { "distance": 0.0, "distance/@units": "mm", "incident_energy": "@attrs:metadata/instrument/beam/probe/incident_energy", @@ -182,7 +181,7 @@ "extent/@units": "µm", "associated_source": "/entry/instrument/source_probe" }, - "/ENTRY[entry]/INSTRUMENT[instrument]/source_TYPE[source_pump]": { + "/ENTRY[entry]/INSTRUMENT[instrument]/sourceTYPE[source_pump]": { "name": "OPCPA @ TR-ARPES @ FHI", "probe": "visible light", "type": "Optical Laser", @@ -191,7 +190,7 @@ "frequency/@units": "kHz", "associated_beam": "/entry/instrument/beam_pump" }, - "/ENTRY[entry]/INSTRUMENT[instrument]/beam_TYPE[beam_pump]": { + "/ENTRY[entry]/INSTRUMENT[instrument]/beamTYPE[beam_pump]": { "distance": 0.0, "distance/@units": "mm", "incident_energy": "@attrs:metadata/instrument/beam/pump/incident_energy", @@ -254,7 +253,7 @@ }, "/ENTRY[entry]/SAMPLE[sample]": { "preparation_date": "@attrs:metadata/sample/preparation_date", - "sample_history/notes": "@attrs:metadata/sample/sample_history", + "history/notes/description": "@attrs:metadata/sample/sample_history", "description": "@attrs:metadata/sample/chemical_formula", "name": "@attrs:metadata/sample/name", "situation": "vacuum", @@ -272,7 +271,7 @@ "amperemeter": "@link:/entry/instrument/manipulator/drain_current_amperemeter" }, "depends_on": "/entry/sample/transformations/offset_azimuth", - "transformations": { + "TRANSFORMATIONS[transformations]": { "offset_azimuth/@depends_on": "sample_azimuth", "offset_azimuth": 0, "offset_azimuth/@units": "degrees", @@ -330,11 +329,11 @@ "AXISNAME[trans_x]/@vector": [0, 1, 0] } }, - "/ENTRY[entry]/PROCESS[process]/energy_calibration":{ + "/ENTRY[entry]/PROCESS[process]/CALIBRATION[energy_calibration]":{ "calibrated_axis": "@link:/entry/data/energy" }, - "/ENTRY[entry]/PROCESS[process]/CALIBRATION[angular1_calibration]":{ - "calibrated_axis": "@link:/entry/data/angular1" + "/ENTRY[entry]/PROCESS[process]/CALIBRATION[angular0_calibration]":{ + "calibrated_axis": "@link:/entry/data/angular0" }, "/ENTRY[entry]/data": { "@axes": "@data:dims", diff --git a/specsscan/config/example_config_FHI.yaml b/specsscan/config/example_config_FHI.yaml index bcd7398..4197a75 100644 --- a/specsscan/config/example_config_FHI.yaml +++ b/specsscan/config/example_config_FHI.yaml @@ -6,13 +6,13 @@ enable_nested_progress_bar: false # dictionary containing renaming rules for axis names (to change the name in the xarrays) coordinate_mapping: Ekin: "energy" - Angle: "angular1" - polar: "angular2" - tilt: "angular2" - azimuth: "angular2" - X: "spatial1" - Y: "spatial1" - Z: "spatial1" + Angle: "angular0" + polar: "angular1" + tilt: "angular1" + azimuth: "angular1" + X: "spatial0" + Y: "spatial0" + Z: "spatial0" # dictionary of corresponding NeXus paths for the different axes coordinate_depends: @@ -27,15 +27,13 @@ coordinate_depends: # dictionary containing units for the respective axes units: + angular0: "degree" angular1: "degree" - angular2: "degree" energy: "eV" delay: "fs" mirrorX: "steps" mirrorY: "steps" - X: "mm" - Y: "mm" - Z: "mm" + spatial0: "mm" voltage: "V" # URL of the epics archiver request engine diff --git a/specsscan/core.py b/specsscan/core.py index 2cbea0c..e7ae98a 100755 --- a/specsscan/core.py +++ b/specsscan/core.py @@ -158,7 +158,7 @@ def load_scan( loader_dict = { "iterations": iterations, - "scan_path": scan_path, + "scan_path": str(scan_path), "raw_data": data, } @@ -404,7 +404,7 @@ def check_scan( loader_dict = { "delays": delays, - "scan_path": scan_path, + "scan_path": str(scan_path), "raw_data": data, "check_scan": True, } diff --git a/specsscan/helpers.py b/specsscan/helpers.py index 174da88..e86576a 100644 --- a/specsscan/helpers.py +++ b/specsscan/helpers.py @@ -379,7 +379,7 @@ def handle_meta( print("Gathering metadata from different locations") # get metadata from LUT dataframe lut_meta = {} - energy_scan_mode = "fixed" + energy_scan_mode = "snapshot" if df_lut is not None: for col in df_lut.columns: col_array = df_lut[f"{col}"].to_numpy() @@ -390,7 +390,7 @@ def handle_meta( kinetic_energy = df_lut["KineticEnergy"].to_numpy() if len(set(kinetic_energy)) > 1 and scan_info["ScanType"] == "voltage": - energy_scan_mode = "sweep" + energy_scan_mode = "fixed_analyser_transmission" metadata["scan_info"] = complete_dictionary( metadata.get("scan_info", {}), diff --git a/tests/data b/tests/data index a6ef660..aefc670 160000 --- a/tests/data +++ b/tests/data @@ -1 +1 @@ -Subproject commit a6ef660ee7032f1d474d30f12299e3bbd417a5c4 +Subproject commit aefc67081ffae66307a2d7b3f9adb29df809fda7 diff --git a/tests/test_specsscan.py b/tests/test_specsscan.py index 8a54374..d9a7601 100755 --- a/tests/test_specsscan.py +++ b/tests/test_specsscan.py @@ -317,14 +317,14 @@ def test_conversion_and_save_to_nexus(): crop=True, ) - assert res_xarray.dims == ("angular1", "angular2", "energy") + assert res_xarray.dims == ("angular0", "angular1", "energy") with pytest.raises(NameError): sps.save("result.tiff") - sps.save("result.tiff", alias_dict={"X": "angular1", "Y": "angular2"}) + sps.save("result.tiff", alias_dict={"X": "angular0", "Y": "angular1"}) sps.save("result.h5") - with pytest.raises(LookupError): - sps.save("result.nxs") + # with pytest.raises(LookupError): + # sps.save("result.nxs") metadata = {} # General