From 2d6b7e6e1cbe883fa5eae2c932e8cf2fc156cadf Mon Sep 17 00:00:00 2001 From: Ron Hildebrandt Date: Tue, 10 Dec 2024 12:55:27 +0100 Subject: [PATCH] remove config files and specify to find file for witec --- src/pynxtools_raman/reader.py | 6 ++- tests/data/rod/config_file_rod.json | 46 ----------------- tests/data/witec/config_file_witec.json | 65 ------------------------- 3 files changed, 4 insertions(+), 113 deletions(-) delete mode 100644 tests/data/rod/config_file_rod.json delete mode 100644 tests/data/witec/config_file_witec.json diff --git a/src/pynxtools_raman/reader.py b/src/pynxtools_raman/reader.py index b23acf1..543cd88 100644 --- a/src/pynxtools_raman/reader.py +++ b/src/pynxtools_raman/reader.py @@ -110,8 +110,6 @@ def read( return template def handle_rod_file(self, filepath) -> Dict[str, Any]: - print("HANDLE ROD") - # specify default config file for rod files reader_dir = Path(__file__).parent self.config_file = reader_dir.joinpath("config", "config_file_rod.json") # pylint: disable=invalid-type-comment @@ -161,6 +159,10 @@ def handle_txt_file(self, filepath): Read a .txt file from Witec Alpha Raman spectrometer and save the header and measurement data. """ + # specify default config file + reader_dir = Path(__file__).parent + self.config_file = reader_dir.joinpath("config", "config_file_witec.json") # pylint: disable=invalid-type-comment + self.raman_data = parse_txt_file(self, filepath) self.post_process = post_process_witec.__get__(self, RamanReader) diff --git a/tests/data/rod/config_file_rod.json b/tests/data/rod/config_file_rod.json deleted file mode 100644 index ed49f98..0000000 --- a/tests/data/rod/config_file_rod.json +++ /dev/null @@ -1,46 +0,0 @@ -{ - "/ENTRY[entry]/INSTRUMENT[instrument]/scattering_configuration": "@data:_raman_measurement_device.direction_polarization", - "/ENTRY[entry]/INSTRUMENT[instrument]/beam_incident/wavelength": "@data:_raman_measurement_device.excitation_laser_wavelength", - "/ENTRY[entry]/INSTRUMENT[instrument]/beam_incident/wavelength/@units": "nm", - "/ENTRY[entry]/INSTRUMENT[instrument]/beam_incident/average_power": "@data:_raman_measurement_device.power_on_sample", - "/ENTRY[entry]/INSTRUMENT[instrument]/beam_incident/average_power/@units": "mW", - "/ENTRY[entry]/INSTRUMENT[instrument]/beam_incident/extent": "@data:_raman_measurement_device.spot_size", - "/ENTRY[entry]/INSTRUMENT[instrument]/beam_incident/extent/@units": "µm", - "/ENTRY[entry]/INSTRUMENT[instrument]/beam_incident/parameter_reliability":"nominal", - "/ENTRY[entry]/INSTRUMENT[instrument]/detector_TYPE[detector_ccd]/count_time/@units": "s", - "/ENTRY[entry]/INSTRUMENT[instrument]/detector_TYPE[detector_ccd]/count_time": "@data:_raman_measurement.integration_time", - "/ENTRY[entry]/INSTRUMENT[instrument]/detector_TYPE[detector_ccd]/detector_channel_type":"single-channel", - "/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source_532nmlaser]/type": "@data:_raman_measurement_device.excitation_laser_type", - "/ENTRY[entry]/INSTRUMENT[instrument]/FABRICATION[device_information]/vendor":"@data:_raman_measurement_device.company", - "/ENTRY[entry]/INSTRUMENT[instrument]/FABRICATION[device_information]/model": "@data:_raman_measurement_device.model", - "/ENTRY[entry]/INSTRUMENT[instrument]/LENS_OPT[objective_lens]/type": "@data:_raman_measurement_device.optics_type", - "/ENTRY[entry]/INSTRUMENT[instrument]/LENS_OPT[objective_lens]/magnification": "@data:_raman_measurement_device.microscope_objective_magnification", - "/ENTRY[entry]/INSTRUMENT[instrument]/LENS_OPT[objective_lens]/numerical_aperture": "@data:_raman_measurement_device.microscope_numerical_aperture", - "/ENTRY[entry]/INSTRUMENT[instrument]/MONOCHROMATOR[monochromator]/grating/period": "@data:_raman_measurement_device.diffraction_grating", - "/ENTRY[entry]/INSTRUMENT[instrument]/MONOCHROMATOR[monochromator]/grating/period/@units": "lines/mm", - "/ENTRY[entry]/SAMPLE[sample]/name":"@data:_chemical_name_systematic", - "/ENTRY[entry]/SAMPLE[sample]/physical_form":"@data:_[local]_chemical_compound_state", - "/ENTRY[entry]/SAMPLE[sample]/chemical_formula":"@data:_chemical_formula_structural", - "/ENTRY[entry]/SAMPLE[sample]/ENVIRONMENT[medium]/sample_medium":"@data:_raman_measurement.environment", - "/ENTRY[entry]/SAMPLE[sample]/ENVIRONMENT[env_temperature]/SENSOR[temperature_sensor]/measurement":"temperature", - "/ENTRY[entry]/SAMPLE[sample]/ENVIRONMENT[env_temperature]/SENSOR[temperature_sensor]/value":"@data:_raman_measurement.temperature", - "/ENTRY[entry]/SAMPLE[sample]/ENVIRONMENT[env_temperature]/SENSOR[temperature_sensor]/value/@units":"K", - "/ENTRY[entry]/SAMPLE[sample]/ENVIRONMENT[env_pressure]/SENSOR[sensor]/measurement":"pressure", - "/ENTRY[entry]/SAMPLE[sample]/ENVIRONMENT[env_pressure]/SENSOR[sensor]/value":"@data:_raman_measurement.pressure", - "/ENTRY[entry]/SAMPLE[sample]/ENVIRONMENT[env_pressure]/SENSOR[sensor]/value/@units":"kPa", - "/ENTRY[entry]/definition/@url": "Remove_this_if_pynxtools_issue_#469_is_solved", - "/ENTRY[entry]/experiment_type": "Raman spectroscopy", - "/ENTRY[entry]/raman_experiment_type": "other", - "/ENTRY[entry]/title": "@data:_chemical_name_mineral", - "/ENTRY[entry]/start_time": "@data:_raman_measurement.datetime_initiated", - "/ENTRY[entry]/@default": "data", - "/ENTRY[entry]/DATA[data]/@signal": "y_values", - "/ENTRY[entry]/DATA[data]/y_values": "@data:_raman_spectrum.intensity", - "/ENTRY[entry]/DATA[data]/y_values/@units": "arb. units", - "/ENTRY[entry]/DATA[data]/y_values/@long_name": "Intensity", - "/ENTRY[entry]/DATA[data]/@axes":"x_values_raman", - "/ENTRY[entry]/DATA[data]/x_values_raman/@long_name": "Raman Shift", - "/ENTRY[entry]/DATA[data]/x_values_raman": "@data:_raman_spectrum.raman_shift", - "/ENTRY[entry]/DATA[data]/x_values_raman/@units": "1/cm" - } - diff --git a/tests/data/witec/config_file_witec.json b/tests/data/witec/config_file_witec.json deleted file mode 100644 index e812abc..0000000 --- a/tests/data/witec/config_file_witec.json +++ /dev/null @@ -1,65 +0,0 @@ -{ - "/ENTRY[entry]/INSTRUMENT[instrument]/scattering_configuration": "@eln", - "/ENTRY[entry]/INSTRUMENT[instrument]/beam_incident/wavelength": "@eln", - "/ENTRY[entry]/INSTRUMENT[instrument]/beam_incident/wavelength/@units": "@eln", - "/ENTRY[entry]/INSTRUMENT[instrument]/beam_incident/parameter_reliability": "@eln", - "/ENTRY[entry]/INSTRUMENT[instrument]/beam_incident/average_power": "@eln", - "/ENTRY[entry]/INSTRUMENT[instrument]/beam_incident/average_power/@units": "@eln", - "/ENTRY[entry]/INSTRUMENT[instrument]/beam_incident/associated_source": "@eln", - "/ENTRY[entry]/INSTRUMENT[instrument]/detector_TYPE[detector_ccd]/detector_channel_type": "@eln", - "/ENTRY[entry]/INSTRUMENT[instrument]/detector_TYPE[detector_ccd]/count_time/@units": "@eln", - "/ENTRY[entry]/INSTRUMENT[instrument]/detector_TYPE[detector_ccd]/count_time": "@eln", - "/ENTRY[entry]/INSTRUMENT[instrument]/detector_TYPE[detector_ccd]/number_of_cycles": "@eln", - "/ENTRY[entry]/INSTRUMENT[instrument]/detector_TYPE[detector_ccd]/number_of_cycles/@units": "@eln", - "/ENTRY[entry]/INSTRUMENT[instrument]/detector_TYPE[detector_ccd]/detector_type": "@eln", - "/ENTRY[entry]/INSTRUMENT[instrument]/detector_TYPE[detector_ccd]/FABRICATION[device_information]/model": "@eln", - "/ENTRY[entry]/INSTRUMENT[instrument]/detector_TYPE[detector_ccd]/FABRICATION[device_information]/IDENTIFIER[identifier]/identifier": "@eln", - "/ENTRY[entry]/INSTRUMENT[instrument]/detector_TYPE[detector_ccd]/FABRICATION[device_information]/IDENTIFIER[identifier]/service": "@eln", - "/ENTRY[entry]/INSTRUMENT[instrument]/detector_TYPE[detector_ccd]/detector_number": "@eln", - "/ENTRY[entry]/INSTRUMENT[instrument]/detector_TYPE[detector_ccd]/gain_setting": "@eln", - "/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source_532nmlaser]/type": "@eln", - "/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source_532nmlaser]/power": "@eln", - "/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source_532nmlaser]/power/@units": "@eln", - "/ENTRY[entry]/INSTRUMENT[instrument]/FABRICATION[device_information]/vendor": "@eln", - "/ENTRY[entry]/INSTRUMENT[instrument]/FABRICATION[device_information]/model": "@eln", - "/ENTRY[entry]/INSTRUMENT[instrument]/LENS_OPT[objective_lens]/type": "@eln", - "/ENTRY[entry]/INSTRUMENT[instrument]/LENS_OPT[objective_lens]/FABRICATION[device_information]/vendor": "@eln", - "/ENTRY[entry]/INSTRUMENT[instrument]/LENS_OPT[objective_lens]/FABRICATION[device_information]/model": "@eln", - "/ENTRY[entry]/INSTRUMENT[instrument]/LENS_OPT[objective_lens]/magnification": "@eln", - "/ENTRY[entry]/INSTRUMENT[instrument]/LENS_OPT[objective_lens]/numerical_aperture": "@eln", - "/ENTRY[entry]/INSTRUMENT[instrument]/MONOCHROMATOR[monochromator]/device_information/model": "@eln", - "/ENTRY[entry]/INSTRUMENT[instrument]/MONOCHROMATOR[monochromator]/grating/period": "@eln", - "/ENTRY[entry]/INSTRUMENT[instrument]/MONOCHROMATOR[monochromator]/grating/period/@units": "@eln", - "/ENTRY[entry]/INSTRUMENT[instrument]/MONOCHROMATOR[monochromator]/wavelength": "@eln", - "/ENTRY[entry]/INSTRUMENT[instrument]/MONOCHROMATOR[monochromator]/wavelength/@units": "@eln", - "/ENTRY[entry]/INSTRUMENT[instrument]/SENSOR[temperature_sensor]/attached_to": "@eln", - "/ENTRY[entry]/INSTRUMENT[instrument]/SENSOR[temperature_sensor]/measurement": "@eln", - "/ENTRY[entry]/INSTRUMENT[instrument]/SENSOR[temperature_sensor]/value": "@eln", - "/ENTRY[entry]/INSTRUMENT[instrument]/SENSOR[temperature_sensor]/value/@units": "@eln", - "/ENTRY[entry]/SAMPLE[sample]/name": "@eln", - "/ENTRY[entry]/SAMPLE[sample]/atom_types": "@eln", - "/ENTRY[entry]/USER[user]/address": "@eln", - "/ENTRY[entry]/USER[user]/affiliation": "@eln", - "/ENTRY[entry]/USER[user]/email": "@eln", - "/ENTRY[entry]/USER[user]/name": "@eln", - "/ENTRY[entry]/experiment_description": "@eln", - "/ENTRY[entry]/experiment_type": "@eln", - "/ENTRY[entry]/raman_experiment_type": "@eln", - "/ENTRY[entry]/title": "@eln", - "/ENTRY[entry]/start_time": "@eln", - "/ENTRY[entry]/definition": "@eln", - "/ENTRY[entry]/definition/@url": "@eln", - "/ENTRY[entry]/@default": "data", - "/ENTRY[entry]/DATA[data]/@signal": "y_values", - "/ENTRY[entry]/DATA[data]/y_values": "@data:data/y_values", - "/ENTRY[entry]/DATA[data]/x_values": "@data:data/x_values", - "/ENTRY[entry]/DATA[data]/y_values/@units": "@eln:/ENTRY[entry]/data/unit_y", - "/ENTRY[entry]/DATA[data]/x_values/@units": "@eln:/ENTRY[entry]/data/unit_x", - "/ENTRY[entry]/DATA[data]/y_values/@long_name": "@eln:/ENTRY[entry]/data/longname_y", - "/ENTRY[entry]/DATA[data]/x_values/@long_name": "@eln:/ENTRY[entry]/data/longname_x", - "/ENTRY[entry]/DATA[data]/@axes":"x_values_raman", - "/ENTRY[entry]/DATA[data]/x_values_raman/@long_name": "@eln:/ENTRY[entry]/data/longname_x_raman", - "/ENTRY[entry]/DATA[data]/x_values_raman": "@data:data/x_values_raman", - "/ENTRY[entry]/DATA[data]/x_values_raman/@units": "1/cm" - } -