diff --git a/examples/thermo_fischer/jdx/README.md b/examples/thermo_fischer/jdx/README.md new file mode 100644 index 0000000..208550f --- /dev/null +++ b/examples/thermo_fischer/jdx/README.md @@ -0,0 +1,12 @@ +## WITEC example Raman Multiformat Reader +This is an example dataset to convert a .txt file +(exported ASCII file, Si-wafer-Raman-Spectrum-1.txt) with the addition of a ELN +data file (eln_data.yaml) to a NeXus file. + +## How to use +- 1. Go into the root folder of this repository (default "pynxtools-raman") +- 2. Copy and paste: + ``` + dataconverter examples/thermo_fischer/jdx/dxr_sucrose780.JDX src/pynxtools_raman/config/config_file_thermo_fischer.json --reader raman --nxdl NXraman --output examples/thermo_fischer/jdx/tfs_example_neuxs.nxs + ``` +- 3. A new file should be created at "examples/thermo_fischer/jdx/tfs_example_neuxs.nxs". \ No newline at end of file diff --git a/examples/thermo_fischer/jdx/dxr_sucrose780.JDX b/examples/thermo_fischer/jdx/dxr_sucrose780.JDX new file mode 100644 index 0000000..6d71dd6 --- /dev/null +++ b/examples/thermo_fischer/jdx/dxr_sucrose780.JDX @@ -0,0 +1,251 @@ +##TITLE=bogus DXR sucrose 780 for installer testing +##JCAMP-DX=5.01 $$ Nicolet v. 521 +##DATATYPE=RAMAN SPECTRUM +##ORIGIN=TFS +##OWNER=Nicolet +##LONGDATE=2005/12/14 +##TIME=17:54:26 +##SPECTROMETER/DATA SYSTEM=Almega +##DATA PROCESSING= +Wavelength->Wavenumber +##COMMENTS= +Number of sample scans: 2 +Collection length: 22.00 sec +Number of background scans: 32 +Raman laser frequency: 12827.97 cm-1 +Number of rejected sample scans: 0 +Number of rejected background scans: 0 +##XUNITS=RAMAN SHIFT(1/CM) +##YUNITS=RAMAN INTENSITY +##FIRSTX=102.020508 +##LASTX=3480.694336 +##FIRSTY=610.938049 +##MAXX=3480.694336 +##MINX=102.020508 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dispersiv/dxr_sucrose780.WMF differ diff --git a/src/pynxtools_raman/config/config_file_thermo_fischer.json b/src/pynxtools_raman/config/config_file_thermo_fischer.json new file mode 100644 index 0000000..7fd440a --- /dev/null +++ b/src/pynxtools_raman/config/config_file_thermo_fischer.json @@ -0,0 +1,28 @@ +{ + "/ENTRY[entry]/INSTRUMENT[instrument]/beam_incident/wavelength": "@data:Raman laser wavelength", + "/ENTRY[entry]/INSTRUMENT[instrument]/beam_incident/wavelength/@units": "@data:Raman laser wavelength_unit", + "/ENTRY[entry]/INSTRUMENT[instrument]/beam_incident/parameter_reliability":"nominal", + "/ENTRY[entry]/INSTRUMENT[instrument]/detector_TYPE[detector_ccd]/count_time/@units": "@data:Collection length_unit", + "/ENTRY[entry]/INSTRUMENT[instrument]/detector_TYPE[detector_ccd]/count_time": "@data:Collection length", + "/ENTRY[entry]/INSTRUMENT[instrument]/detector_TYPE[detector_ccd]/detector_channel_type":"multichannel", + "/ENTRY[entry]/INSTRUMENT[instrument]/detector_TYPE[detector_ccd]/DATA[bkg_scan_number]":"@data:Number of background scans", + "/ENTRY[entry]/INSTRUMENT[instrument]/detector_TYPE[detector_ccd]/DATA[sample_scan_number]":"@data:Number of sample scans", + "/ENTRY[entry]/INSTRUMENT[instrument]/FABRICATION[device_information]/vendor":"Thermo Fisher Scientific", + "/ENTRY[entry]/INSTRUMENT[instrument]/FABRICATION[device_information]/model": "@data:##SPECTROMETER/DATA SYSTEM", + "/ENTRY[entry]/INSTRUMENT[instrument]/software_TYPE[software_jdx_processing]/program": "@data:##JCAMP-DX", + "/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:##TITLE", + "/ENTRY[entry]/start_time": "@data:##LONGDATE_AND_TIME", + "/ENTRY[entry]/@default": "data", + "/ENTRY[entry]/DATA[data]/@signal": "y_values", + "/ENTRY[entry]/DATA[data]/y_values": "@data:data_y_averaged_scaled", + "/ENTRY[entry]/DATA[data]/y_values/@units": "@data:##YUNITS", + "/ENTRY[entry]/DATA[data]/y_values/@long_name": "@data:##YUNITS", + "/ENTRY[entry]/DATA[data]/@axes":"x_values_raman", + "/ENTRY[entry]/DATA[data]/x_values_raman/@long_name": "@data:##XUNITS", + "/ENTRY[entry]/DATA[data]/x_values_raman": "@data:data_x", + "/ENTRY[entry]/DATA[data]/x_values_raman/@units": "@data:##XUNITS" + } + diff --git a/src/pynxtools_raman/reader.py b/src/pynxtools_raman/reader.py index 5021697..0282053 100644 --- a/src/pynxtools_raman/reader.py +++ b/src/pynxtools_raman/reader.py @@ -30,7 +30,7 @@ from pynxtools_raman.rod.rod_reader import RodParser from pynxtools_raman.witec.witec_reader import post_process_witec from pynxtools_raman.witec.witec_reader import parse_txt_file - +from pynxtools_raman.thermo_fischer.thermo_fischer_reader import parse_jdx_file logger = logging.getLogger("pynxtools") @@ -60,6 +60,7 @@ def __init__(self, *args, **kwargs): ".txt": self.handle_txt_file, ".json": self.set_config_file, ".rod": self.handle_rod_file, + ".jdx": self.handle_jdx_file, } def set_config_file(self, file_path: Path) -> Dict[str, Any]: @@ -79,6 +80,16 @@ def handle_eln_file(self, file_path: str) -> Dict[str, Any]: return {} + def handle_jdx_file(self, filepath) -> Dict[str, Any]: + reader_dir = Path(__file__).parent + self.config_file = reader_dir.joinpath( + "config", "config_file_thermo_fischer.json" + ) # pylint: disable=invalid-type-comment + + self.raman_data = parse_jdx_file(filepath) + # print(self.raman_data) + return {} + def handle_rod_file(self, filepath) -> Dict[str, Any]: # specify default config file for rod files reader_dir = Path(__file__).parent diff --git a/src/pynxtools_raman/thermo_fischer/__init__.py b/src/pynxtools_raman/thermo_fischer/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/src/pynxtools_raman/thermo_fischer/thermo_fischer_reader.py b/src/pynxtools_raman/thermo_fischer/thermo_fischer_reader.py new file mode 100644 index 0000000..a44f124 --- /dev/null +++ b/src/pynxtools_raman/thermo_fischer/thermo_fischer_reader.py @@ -0,0 +1,107 @@ +import numpy as np +import datetime + + +def parse_jdx_file(filepath): + """ + Read a .txt file from Witec Alpha Raman spectrometer and return a data dictionary + which contains Raman shift and Intensity + """ + data_dict = {} + + with open(filepath, "r") as file: + data = file.readlines() + + # Separate metadata and measurement data + jdx_metadata = [] + jdx_measurement_data = [] + is_measurement = False + + for line in data: + if line.startswith("##XYDATA"): + is_measurement = True + elif line.startswith("##END"): + is_measurement = False + elif not is_measurement: + jdx_metadata.append(line.replace("\n", "")) + else: + jdx_measurement_data.append(line.replace("\n", "")) + + # extract float like measruement data colums: + jdx_data_list = [] + + for line in jdx_measurement_data: + string_list = line.split() + float_list = [float(item) for item in string_list] + jdx_data_list.append(float_list) + + # Transform: [[A, B], [C, D], [E, F]] into [[A, C, E], [B, D, F]] + jdx_data_list = [list(item) for item in zip(*jdx_data_list)] + + column_counter = 0 + for column in jdx_data_list: + if column_counter == 0: + data_dict["data_x"] = column + if column_counter > 0: + data_dict[f"data_y_{column_counter}"] = column + column_counter = column_counter + 1 + + # extract key value pair from meta data: + for i in range(len(jdx_metadata)): + # Metadata, always starts with ## + if jdx_metadata[i].startswith("##"): + key, value = jdx_metadata[i].split("=") + data_dict[key] = value + # this covers multi-line meta data such as comments or similar. This + # is appended to a list and then added to the dictionary + else: + if key in data_dict and isinstance(data_dict[key], list): + data_dict[key].append(jdx_metadata[i]) + else: + data_dict[key] = [jdx_metadata[i]] + + comment = data_dict["##COMMENTS"] + for entry in comment: + key, value = entry.split(":") + unit = None + if value.startswith(" "): # Check if the string starts with a space + value = value[1:] + if value.find(" ") != -1: + value, unit = value.split(" ") + if key == "Number of sample scans": + data_dict["Number of sample scans"] = int(value) + if key == "Collection length": + data_dict["Collection length"] = float(value) + data_dict["Collection length_unit"] = unit + if key == "Number of background scans": + data_dict["Number of background scans"] = int(value) + data_dict["Number of background scans_unit"] = unit + if key == "Raman laser frequency": + data_dict["Raman laser wavelength"] = 1e7 / float(value) + data_dict["Raman laser wavelength_unit"] = "nm" # assumed input is 1/cm + if key == "Number of rejected sample scans": + data_dict["Number of rejected sample scans"] = int(value) + if key == "Number of rejected background scans": + data_dict["Number of rejected background scans"] = int(value) + + time_date = data_dict["##LONGDATE"] + time_hour = data_dict["##TIME"] + date_time_oject = datetime.datetime.strptime( + f"{time_date} {time_hour}", "%Y/%m/%d %H:%M:%S" + ) + tzinfo = datetime.timezone.utc + date_time_oject = date_time_oject.replace(tzinfo=tzinfo) + data_dict["##LONGDATE_AND_TIME"] = date_time_oject.isoformat() + + number_y_colums = sum(1 for key in data_dict if "data_y_" in key) + y_average = np.zeros(len(data_dict[f"data_x"])) + + for i in range(number_y_colums): + y_average = np.array(data_dict[f"data_y_{i+1}"]) + y_average + + raman_counts = ( + np.array(y_average) / int(number_y_colums) * float(data_dict["##YFACTOR"]) + ).tolist() + data_dict["data_y_averaged_scaled"] = raman_counts + + return data_dict