xrdpattern: Merged PowderExperiment into xrdpattern

tests/t_parsing/t_parser.py

@@ -21,17 +21,10 @@ def test_report_ok(self):
         print(f'Parsing report: {as_str}')
 
     def test_metadata_ok(self):
-        metadata = self.pattern.metadata
-        properties = [metadata.anode_material, metadata.measurement_date]
-        print(f'anode material {metadata.anode_material}')
-        print(f'measurement date {metadata.measurement_date}')
-
-        for prop in properties:
-            self.assertIsNotNone(obj=prop)
-
-        primary_wavelength = metadata.primary
-        secondary_wavelength = metadata.secondary
-        ratio = metadata.ratio
+        metadata = self.pattern.experiment
+        primary_wavelength = metadata.primary_wavelength
+        secondary_wavelength = metadata.secondary_wavelength
+        ratio = metadata.artifacts.secondary_to_primary
         print(f'prim, sec, ratio {primary_wavelength}, {secondary_wavelength}, {ratio}')
 
         for prop in [primary_wavelength, secondary_wavelength, ratio]:

tests/t_pattern/t_xrdpattern.py

@@ -35,7 +35,7 @@ def test_data_ok(self):
     def test_from_angle_data(self):
         angles = [1.0, 2.0, 3.0]
         intensities = [10.0, 20.0, 100.0]
-        pattern = XrdPattern.from_intensitiy_map(angles=angles, intensities=intensities)
+        pattern = XrdPattern.from_intensitiy_map(two_theta_values=angles, intensities=intensities)
         self.check_data_ok(*pattern.get_pattern_data(apply_standardization=False))
 
 if __name__ == "__main__":

xrdpattern/core/__init__.py

@@ -1,2 +1 @@
-from .metadata import Metadata
-from .pattern_info import PatternInfo
+from .pattern_data import PatternData

xrdpattern/core/pattern_info.py → xrdpattern/core/pattern_data.py

@@ -5,26 +5,22 @@
 from holytools.abstract import JsonDataclass
 from dataclasses import dataclass, fields
 from typing import Optional
-from .metadata import Metadata
+
+from xrdpattern.powder import PowderExperiment
 
 # -------------------------------------------
 
 @dataclass
-class PatternInfo(JsonDataclass):
+class PatternData(JsonDataclass):
     two_theta_values : list[float]
     intensities : list[float]
-    metadata: Metadata
+    experiment : PowderExperiment
     name : Optional[str] = None
 
-    def get_wavelength(self, primary : bool = True) -> Optional[float]:
-        wavelength = self.metadata.primary if primary else self.metadata.secondary
-        return wavelength
-
-    def set_wavelength(self, new_wavelength : float, primary : bool = True):
-        if primary:
-            self.metadata.primary = new_wavelength
-        else:
-            self.metadata.secondary = new_wavelength
+    @classmethod
+    def from_intensitiy_map(cls, two_theta_values: list[float], intensities: list[float]) -> PatternData:
+        metadata = PowderExperiment.make_empty()
+        return cls(two_theta_values=two_theta_values, intensities=intensities, experiment=metadata)
 
     def to_dict(self):
         return {f.name: getattr(self, f.name) for f in fields(self)}
@@ -51,15 +47,14 @@ def get_standardized_map(self, start_val : float, stop_val : float, num_entries
         return std_angles,std_intensities
 
 
-    def __eq__(self, other : PatternInfo):
-        if not isinstance(other, PatternInfo):
+    def __eq__(self, other : PatternData):
+        if not isinstance(other, PatternData):
             return False
 
         angles_equal = self.two_theta_values == other.two_theta_values
         intensities_equal = self.intensities == other.intensities
-        metadata_equal = self.metadata == other.metadata
 
-        return angles_equal and intensities_equal and metadata_equal
+        return angles_equal and intensities_equal
 
 
 if __name__ == '__main__':

xrdpattern/parsing/csv/csv_read.py

@@ -5,7 +5,7 @@
 
 from holytools.abstract import SelectableEnum
 
-from xrdpattern.core import Metadata, PatternInfo
+from xrdpattern.core import PatternData
 from .table_selector import TableSelector, TextTable, NumericalTable
 
 
@@ -44,7 +44,7 @@ def as_matrix(self, fpath : str) -> NumericalTable:
         return TableSelector.get_numerical_subtable(table=table)
 
 
-    def read_csv(self, fpath: str) -> list[PatternInfo]:
+    def read_csv(self, fpath: str) -> list[PatternData]:
         matrix = self.as_matrix(fpath=fpath)
         x_axis_row = matrix.get_data(row=0)
         data_rows = [matrix.get_data(row=row) for row in range(1, matrix.get_row_count())]
@@ -63,7 +63,7 @@ def read_csv(self, fpath: str) -> list[PatternInfo]:
             two_theta_degs = x_axis_row
 
         for intensities in data_rows:
-            new = PatternInfo(two_theta_values=two_theta_degs, intensities=intensities, metadata=Metadata.make_empty())
+            new = PatternData.from_intensitiy_map(two_theta_values=two_theta_degs, intensities=intensities)
             pattern_infos.append(new)
 
         x_axis_type = 'QValues' if is_qvalues else 'TwoThetaDegs'

xrdpattern/parsing/parser.py

@@ -4,10 +4,13 @@
 from typing import Optional
 from dataclasses import dataclass
 from holytools.fsys import SaveManager
-from xrdpattern.core import PatternInfo, Metadata
+from xrdpattern.core import PatternData
 from .data_files import XrdFormat, Formats, get_xylib_repr
 from .csv import CsvParser, Orientation
 from xrdpattern.parsing.stoe import StoeReader
+from ..powder import PowderExperiment
+
+
 # -------------------------------------------
 
 @dataclass
@@ -27,7 +30,7 @@ def __init__(self, parser_options : ParserOptions = ParserOptions()):
     # -------------------------------------------
     # pattern
 
-    def get_pattern_info_list(self, fpath : str) -> list[PatternInfo]:
+    def get_pattern_info_list(self, fpath : str) -> list[PatternData]:
         suffix = SaveManager.get_suffix(fpath)
         if not suffix in Formats.get_allowed_suffixes():
             raise ValueError(f"File {fpath} has unsupported format .{suffix}")
@@ -47,26 +50,26 @@ def get_pattern_info_list(self, fpath : str) -> list[PatternInfo]:
         else:
             raise ValueError(f"Format .{the_format} is not supported")
         for pattern in pattern_infos:
-            if pattern.get_wavelength(primary=True) is None and self.default_wavelength_angstr:
-                pattern.set_wavelength(new_wavelength=self.default_wavelength_angstr)
+            if pattern.experiment.primary_wavelength is None and self.default_wavelength_angstr:
+                pattern.experiment.artifacts.primary_wavelength = self.default_wavelength_angstr
         for info in pattern_infos:
             info.name = os.path.basename(fpath)
         return pattern_infos
 
 
     @staticmethod
-    def from_json(fpath: str) -> PatternInfo:
+    def from_json(fpath: str) -> PatternData:
         with open(fpath, 'r') as file:
             data = file.read()
-            new_pattern = PatternInfo.from_str(json_str=data)
+            new_pattern = PatternData.from_str(json_str=data)
         return new_pattern
 
 
     @staticmethod
-    def from_data_file(fpath: str, format_hint : XrdFormat) -> PatternInfo:
+    def from_data_file(fpath: str, format_hint : XrdFormat) -> PatternData:
         xylib_repr = get_xylib_repr(fpath=fpath, format_hint=format_hint)
         header,data_str = xylib_repr.get_header(), xylib_repr.get_data()
-        metadata = Metadata.from_header_str(header_str=header)
+        metadata = PowderExperiment.from_xylib_header(header_str=header)
 
         angles, intensities= [], []
         data_rows = [row for row in data_str.split('\n') if not row.strip() == '']
@@ -75,11 +78,11 @@ def from_data_file(fpath: str, format_hint : XrdFormat) -> PatternInfo:
             deg, intensity = float(deg_str), float(intensity_str)
             angles.append(deg)
             intensities.append(intensity)
-        return PatternInfo(two_theta_values=angles,intensities=intensities,metadata=metadata)
+        return PatternData(two_theta_values=angles, intensities=intensities, experiment=metadata)
 
 
     @staticmethod
-    def from_csv(fpath : str) -> list[PatternInfo]:
+    def from_csv(fpath : str) -> list[PatternData]:
         if CsvParser.has_two_columns(fpath=fpath):
             orientation = Orientation.VERTICAL
         else:

xrdpattern/parsing/stoe/reader.py

@@ -1,5 +1,7 @@
-from xrdpattern.core import Metadata, PatternInfo
+from xrdpattern.core import PatternData
 from .quantities import Quantity, FloatQuantity, IntegerQuantity
+from ...powder import Artifacts, PowderExperiment
+
 
 class BinaryReader:
     def read(self, fpath : str):
@@ -35,16 +37,17 @@ def read(self, fpath : str):
         super().read_bytes(byte_content=byte_content)
 
 
-    def get_pattern_info(self, fpath : str) -> PatternInfo:
+    def get_pattern_info(self, fpath : str) -> PatternData:
         self.read(fpath=fpath)
-        metadata = Metadata(primary=self.primary_wavelength.get_value(),
-                            secondary=self.secondary_wavelength.get_value(),
-                            ratio=self.ratio.get_value())
+        experiment = PowderExperiment.make_empty()
+        experiment.artifacts = Artifacts(primary_wavelength=self.primary_wavelength.get_value(),
+                                         secondary_wavelength=self.secondary_wavelength.get_value(),
+                                         secondary_to_primary=self.ratio.get_value())
 
         two_theta_values = self._get_x_values()
         intensities = self._get_y_values()
 
-        return PatternInfo(metadata=metadata, two_theta_values=two_theta_values, intensities=intensities)
+        return PatternData(two_theta_values=two_theta_values, intensities=intensities, experiment=experiment)
 
 
     def _get_x_values(self) -> list[float]:

xrdpattern/pattern/pattern.py

@@ -1,16 +1,20 @@
 from __future__ import annotations
-import matplotlib.pyplot as plt
+
 import os
-from uuid import uuid4
 from typing import Optional
-from holytools.fsys import SaveManager
+from uuid import uuid4
+
+import matplotlib.pyplot as plt
 
+from holytools.fsys import SaveManager
+from xrdpattern.core import PatternData
 from xrdpattern.parsing import Parser, ParserOptions
-from xrdpattern.core import PatternInfo, Metadata
 from .pattern_report import PatternReport
+
+
 # -------------------------------------------
 
-class XrdPattern(PatternInfo):
+class XrdPattern(PatternData):
     def plot(self, apply_standardization=True):
         plt.figure(figsize=(10, 6))
         plt.ylabel('Intensity')
@@ -52,11 +56,6 @@ def save(self, fpath : str, force_overwrite : bool = False):
         with open(fpath, 'w') as f:
             f.write(self.to_str())
 
-    @classmethod
-    def from_intensitiy_map(cls, angles: list[float], intensities: list[float]) -> XrdPattern:
-        metadata = Metadata.make_empty()
-        return XrdPattern(two_theta_values=angles, intensities=intensities, metadata=metadata)
-
     # -------------------------------------------
     # get
 
@@ -66,15 +65,11 @@ def get_parsing_report(self, datafile_fpath : str) -> PatternReport:
             pattern_health.add_critical('No data found. Degree over intensity is empty!')
         elif len(self.two_theta_values) < 10:
             pattern_health.add_critical('Data is too short. Less than 10 entries!')
-        if self.get_wavelength(primary=True) is None:
-            pattern_health.add_error('Primary wavelength missing!')
 
-        if self.get_wavelength(primary=False) is None:
+        if self.experiment.primary_wavelength is None:
+            pattern_health.add_error('Primary wavelength missing!')
+        if self.experiment.secondary_wavelength is None:
             pattern_health.add_warning('No secondary wavelength found')
-        if self.metadata.anode_material is None:
-            pattern_health.add_warning('No anode material found')
-        if self.metadata.measurement_date is None:
-            pattern_health.add_warning('No measurement datetime found')
 
         return pattern_health