From 886e4ba95c320a515c0d6f124abb2821dfc0248d Mon Sep 17 00:00:00 2001 From: Lukas Pielsticker <50139597+lukaspie@users.noreply.github.com> Date: Mon, 14 Oct 2024 14:51:55 +0200 Subject: [PATCH] bring in additional changes from SprintNomadBaseSectionEmApmFixes branch --- src/pynxtools_apm/examples/nomad/apm.archive.json | 1 - .../{examples/nomad => nomad/examples}/README.md | 0 src/pynxtools_apm/nomad/examples/apm.archive.json | 1 + .../nomad => nomad/examples}/apm.oasis.specific.yaml | 0 .../nomad => nomad/examples}/downloads.archive.yaml | 0 .../{examples/nomad => nomad/examples}/eln_data.yaml | 8 ++++++++ .../nomad => nomad/examples}/nxapm.schema.archive.yaml | 0 7 files changed, 9 insertions(+), 1 deletion(-) delete mode 100644 src/pynxtools_apm/examples/nomad/apm.archive.json rename src/pynxtools_apm/{examples/nomad => nomad/examples}/README.md (100%) create mode 100644 src/pynxtools_apm/nomad/examples/apm.archive.json rename src/pynxtools_apm/{examples/nomad => nomad/examples}/apm.oasis.specific.yaml (100%) rename src/pynxtools_apm/{examples/nomad => nomad/examples}/downloads.archive.yaml (100%) rename src/pynxtools_apm/{examples/nomad => nomad/examples}/eln_data.yaml (92%) rename src/pynxtools_apm/{examples/nomad => nomad/examples}/nxapm.schema.archive.yaml (100%) diff --git a/src/pynxtools_apm/examples/nomad/apm.archive.json b/src/pynxtools_apm/examples/nomad/apm.archive.json deleted file mode 100644 index 95fe961..0000000 --- a/src/pynxtools_apm/examples/nomad/apm.archive.json +++ /dev/null @@ -1 +0,0 @@ -{"data":{"m_def":"../upload/raw/nxapm.schema.archive.yaml#/definitions/section_definitions/0","reader":"apm","nxdl":"NXapm.nxdl","input_files":["eln_data.yaml","Si.apt","Si.RRNG","apm.oasis.specific.yaml"],"output":"apm.nxs","entry":{"experiment_description":"

Normal

\n

Bold

\n

Italics

","start_time":"2023-06-12T13:57:00+00:00","end_time":"2023-06-12T13:57:00+00:00","run_number":"2121","operation_mode":"apt"},"workflow":{"raw_dat_file":"","hit_dat_file":"","recon_cfg_file":""},"sample":{"alias":"Si","method":"experiment","composition":["Si","Cr 2 +- 0.5","C 50 ppm +- 12"],"grain_diameter":200,"grain_diameter_error":50,"heat_treatment_temperature":600,"heat_treatment_temperature_error":20,"heat_treatment_quenching_rate":150,"heat_treatment_quenching_rate_error":10},"specimen":{"alias":"Si","method":"experiment","preparation_date":"2023-06-12T13:59:00+00:00","is_polycrystalline":false,"is_amorphous":false,"description":"this is a NOMAD example","initial_radius":20,"shank_angle":5},"user":[{"name":"MarkusK"},{"name":"Jesse Smith"}],"instrument":{"status":"success","instrument_name":"LEAP","location":"Denton","nominal_flight_path":1.2,"fabrication_vendor":"Cameca","fabrication_model":"LEAP3000","fabrication_identifier":"12","reflectron_status":"used","base_temperature":20,"chamber_pressure":2e-10,"target_detection_rate":0.8,"pulser":{"pulse_mode":"laser","pulse_frequency":250,"pulse_fraction":0.8,"laser_source":[{"name":"laser1","wavelength":254,"power":12,"pulse_energy":20},{"name":"laser2","wavelength":355,"power":24,"pulse_energy":40}]},"local_electrode_name":"L1"},"reconstruction":{"program":"IVAS","program_version":"3.6.8","protocol_name":"bas","parameter":"kf = 1.8, icf = 3.3","crystallographic_calibration":"n/a","field_of_view":20},"ranging":{"program":"IVAS","program_version":"3.6.8"}}} \ No newline at end of file diff --git a/src/pynxtools_apm/examples/nomad/README.md b/src/pynxtools_apm/nomad/examples/README.md similarity index 100% rename from src/pynxtools_apm/examples/nomad/README.md rename to src/pynxtools_apm/nomad/examples/README.md diff --git a/src/pynxtools_apm/nomad/examples/apm.archive.json b/src/pynxtools_apm/nomad/examples/apm.archive.json new file mode 100644 index 0000000..95c9c44 --- /dev/null +++ b/src/pynxtools_apm/nomad/examples/apm.archive.json @@ -0,0 +1 @@ +{"data":{"m_def":"../upload/raw/nxapm.schema.archive.yaml#/definitions/section_definitions/0","reader":"apm","nxdl":"NXapm","input_files":["eln_data.yaml","Si.apt","Si.RRNG","apm.oasis.specific.yaml"],"output":"apm.nxs","entry":{"experiment_description":"

Normal

\n

Bold

\n

Italics

","start_time":"2023-06-12T13:57:00+00:00","end_time":"2023-06-12T13:57:00+00:00","run_number":"2121","operation_mode":"apt"},"workflow":{"raw_dat_file":"","hit_dat_file":"","recon_cfg_file":""},"sample":{"alias":"Si","method":"experiment","composition":["Si","Cr 2 +- 0.5","C 50 ppm +- 12"],"grain_diameter":200,"grain_diameter_error":50,"heat_treatment_temperature":600,"heat_treatment_temperature_error":20,"heat_treatment_quenching_rate":150,"heat_treatment_quenching_rate_error":10},"specimen":{"alias":"Si","method":"experiment","preparation_date":"2023-06-12T13:59:00+00:00","is_polycrystalline":false,"is_amorphous":false,"description":"this is a NOMAD example","initial_radius":20,"shank_angle":5},"user":[{"name":"MarkusK"},{"name":"Jesse Smith"}],"instrument":{"status":"success","instrument_name":"LEAP","location":"Denton","nominal_flight_path":1.2,"fabrication_vendor":"Cameca","fabrication_model":"LEAP3000","fabrication_identifier":"12","reflectron_status":"used","base_temperature":20,"chamber_pressure":2e-10,"target_detection_rate":0.8,"pulser":{"pulse_mode":"laser","pulse_frequency":250,"pulse_fraction":0.8,"laser_source":[{"name":"laser1","wavelength":254,"power":12,"pulse_energy":20},{"name":"laser2","wavelength":355,"power":24,"pulse_energy":40}]},"local_electrode_name":"L1"},"reconstruction":{"program":"IVAS","program_version":"3.6.8","protocol_name":"bas","parameter":"kf = 1.8, icf = 3.3","crystallographic_calibration":"n/a","field_of_view":20},"ranging":{"program":"IVAS","program_version":"3.6.8"}}} \ No newline at end of file diff --git a/src/pynxtools_apm/examples/nomad/apm.oasis.specific.yaml b/src/pynxtools_apm/nomad/examples/apm.oasis.specific.yaml similarity index 100% rename from src/pynxtools_apm/examples/nomad/apm.oasis.specific.yaml rename to src/pynxtools_apm/nomad/examples/apm.oasis.specific.yaml diff --git a/src/pynxtools_apm/examples/nomad/downloads.archive.yaml b/src/pynxtools_apm/nomad/examples/downloads.archive.yaml similarity index 100% rename from src/pynxtools_apm/examples/nomad/downloads.archive.yaml rename to src/pynxtools_apm/nomad/examples/downloads.archive.yaml diff --git a/src/pynxtools_apm/examples/nomad/eln_data.yaml b/src/pynxtools_apm/nomad/examples/eln_data.yaml similarity index 92% rename from src/pynxtools_apm/examples/nomad/eln_data.yaml rename to src/pynxtools_apm/nomad/examples/eln_data.yaml index ba16e8e..3ae7457 100644 --- a/src/pynxtools_apm/examples/nomad/eln_data.yaml +++ b/src/pynxtools_apm/nomad/examples/eln_data.yaml @@ -81,6 +81,10 @@ sample: - C 3.6 method: experiment alias: Si + identifier: + service: undefined + identifier: 'Si in sample' + is_persistent: false grain_diameter: unit: µm value: 200. @@ -103,6 +107,10 @@ sample: specimen: method: experiment alias: usa_denton_smith_si + identifier: + service: undefined + identifier: 'Si in specimen' + is_persistent: false description: '

normal

bold

diff --git a/src/pynxtools_apm/examples/nomad/nxapm.schema.archive.yaml b/src/pynxtools_apm/nomad/examples/nxapm.schema.archive.yaml similarity index 100% rename from src/pynxtools_apm/examples/nomad/nxapm.schema.archive.yaml rename to src/pynxtools_apm/nomad/examples/nxapm.schema.archive.yaml