initial version of the update pdffit2 interface

easydiffraction/Interfaces/pdffit2.py

@@ -12,6 +12,7 @@
 
 from easydiffraction import Lattice
 from easydiffraction import Phases
+from easydiffraction import Phase
 from easydiffraction import Site
 from easydiffraction import SpaceGroup
 from easydiffraction.calculators.pdffit2 import Pdffit2 as Pdffit2_calc
@@ -140,6 +141,12 @@ def create(self, model) -> List[ItemContainer]:
             self._phase = model
             self.calculator.phases = model
 
+        elif issubclass(t_, Phase):
+            self._phase = model
+            if self.calculator.phases is None:
+                self.calculator.phases = Phases()
+            self.calculator.phases.append(model)
+
         elif issubclass(t_, Sample):
             self.updateCif()
 
@@ -180,6 +187,16 @@ def updateCif(self, *args, **kwargs):
             self.calculator.cif_string = str(self._phase.cif)
         pass
 
+    def updateModelCif(self, cif_string: str):
+        self.calculator.cif_string = cif_string
+
+    def add_phase(self, phases_obj: Phases, phase_obj: Phase) -> None:
+        """
+        Add a phase to the phases object.
+        """
+        self.calculator.phases = phases_obj
+        self.calculator.phases[0].scale = phase_obj.scale.raw_value
+
     @staticmethod
     def __identify(obj):
         return obj.unique_name

easydiffraction/Job.py

@@ -32,8 +32,8 @@
 from easydiffraction.Profiles.P1D import Instrument1DTOFParameters
 from easydiffraction.Profiles.P1D import PolPowder1DParameters
 from easydiffraction.Profiles.P1D import Powder1DParameters
+from easydiffraction.Profiles.P1D import PDFParameters
 
-# from easydiffraction.Profiles.Sample import Sample
 from easydiffraction.sample import Sample
 
 try:
@@ -148,6 +148,10 @@ def __init__(
         self._kwargs['_parameters'] = self.sample.parameters
         self._kwargs['_pattern'] = self.sample.pattern
 
+        # set the appropriate calculator, if needed
+        if self.type.is_pdf:
+            self.calculator = "Pdffit2"
+
 
     @property
     def sample(self) -> Sample:
@@ -169,6 +173,9 @@ def sample(self, value: Union[Sample, None]) -> None:
                 parameters = Instrument1DCWParameters()
             elif self.type.is_tof:
                 parameters = Instrument1DTOFParameters()
+            # special experiment type
+            if self.type.is_pdf:
+                parameters = PDFParameters()
             self._sample = Sample("Sample", parameters=parameters, pattern=pattern)
 
     @property
@@ -420,6 +427,9 @@ def add_experiment_from_file(self, file_url: str) -> None:
         # check the extension first and then call the appropriate method
         if file_url.endswith(".xye"):
             self.experiment.from_xye_file(file_url)
+        elif file_url.endswith(".gr"):
+            # PDF data
+            self.experiment.from_gr_file(file_url)
         else:
             self.experiment.from_cif_file(file_url)
 

easydiffraction/Profiles/Analysis.py

@@ -77,6 +77,14 @@ def fit(self, x: Union[xr.DataArray, np.ndarray],
             return None
         return res
 
+    @property
+    def calculator(self):
+        return self.interface.current_interface_name
+
+    @calculator.setter
+    def calculator(self, value: str):
+        self.interface.switch(value)
+
     @property
     def available_minimizers(self) -> list:
         """

easydiffraction/Profiles/Experiment.py

@@ -8,6 +8,7 @@
 from easyscience.Objects.ObjectClasses import Descriptor
 from easyscience.Objects.ObjectClasses import Parameter
 from gemmi import cif
+from easydiffraction.Interfaces.pdffit2 import readGRData
 
 from easydiffraction.elements.Backgrounds.Point import BackgroundPoint
 from easydiffraction.elements.Backgrounds.Point import PointBackground
@@ -20,6 +21,7 @@
 from easydiffraction.Profiles.P1D import Instrument1DTOFParameters
 from easydiffraction.Profiles.P1D import PolPowder1DParameters
 from easydiffraction.Profiles.P1D import Powder1DParameters
+from easydiffraction.Profiles.P1D import PDFParameters
 
 _DEFAULT_DATA_BLOCK_NO_MEAS_PD_CWL = """data_pnd
 
@@ -326,7 +328,26 @@ def data_from_cif_block(self, block, experiment_name):
         data_x = data['x']
         data_y = data['y']
         data_e = data['e']
+        self.assign_data(data_x, data_y, data_e, experiment_name)
 
+    def from_gr_file(self, file_url, experiment_name=None):
+        """
+        Load a GR file into the experiment.
+        """
+        data = readGRData(file_url)
+        data_x = data[:, 0]
+        data_y = [data[:, 1]]
+        data_e = [data[:, 3]]
+        self.parameters = PDFParameters()
+        if experiment_name is None:
+            experiment_name = 'pdf'
+            self.name = experiment_name
+        self.assign_data(data_x, data_y, data_e, experiment_name)
+
+    def assign_data(self, data_x, data_y, data_e, experiment_name):
+        """
+        Assign data to the experiment store.
+        """
         coord_name = self.job_name + "_" + experiment_name + "_" + self._x_axis_name
 
         self._datastore.store.easyscience.add_coordinate(coord_name, data_x)

easydiffraction/Profiles/JobType.py

@@ -24,13 +24,15 @@ class JobType():
         polarized: pol
         longitudinal polarized: lpa
         spherical polarimetry: snp
+    special experiment type:
+        PDF: pdf
 
     String-based specification can be provided in any order, in any combination.
     Example:
     a = JobType("pd-cwl-unp-1d-xray")
     b = JobType("cwl-unp-neut")
     c = JobType("tof")
-
+    d = JobType("pdf")
     """
     # Sample type
     STR_POWDER = "pd"
@@ -49,6 +51,8 @@ class JobType():
     STR_UPOL = "unp"
     STR_LPOL = "lpa"
     STR_SPOL = "snp"
+    # Special experiment type
+    STR_PDF = "pdf"
 
     # Default values
     DEFAULT_TYPE = "pd-cwl-unp-1d-neut"
@@ -86,7 +90,7 @@ def init_flags(self):
         self._is_unp = False
         self._is_lpa = False
         self._is_snp = False
-
+        self._is_pdf = False
     @property
     def is_pd(self):
         return self._is_pd
@@ -207,6 +211,15 @@ def is_snp(self, value):
         self._is_lpa = not value
         self.validate()
 
+    @property
+    def is_pdf(self):
+        return self._is_pdf
+
+    @is_pdf.setter
+    def is_pdf(self, value):
+        self._is_pdf = value
+        self.validate()
+
     def parse_job_type(self, job_type: str):
         # this will parse the substrings of the job type
         # and amend the existing job type
@@ -238,6 +251,9 @@ def to_typestr(self) -> None:
         elif self._is_snp:
             pol_flag = self.STR_SPOL
         self.type_str = f"{sample_flag}-{beam_flag}-{pol_flag}-{dim_flag}-{radiation_flag}"
+        # special experiment type
+        if self._is_pdf:
+            self.type_str = f"{self.STR_PDF}"
 
     def validate(self):
         """

examples_old/PDF2/Ni_fitting.py

@@ -1,30 +1,17 @@
 
 import os
 
-from easyCore.Fitting.Fitting import Fitter
-from easyDiffractionLib import Phases
-from easyDiffractionLib.Jobs import Powder1DCW
-from easyDiffractionLib.interface import InterfaceFactory as Calculator
-from easyDiffractionLib.Profiles.P1D import PDFParameters
-from easyDiffractionLib.Interfaces.pdffit2 import readGRData
+import easydiffraction as ed
 
 
-# data_fname = "D:\\projects\\easyScience\\easyDiffractionLib\\examples\\PDF\\Ni-xray.gr"
-data_fname = os.path.realpath('Ni-xray.gr')
-data = readGRData(data_fname)
+job = ed.Job(type='pdf')
 
-# phase_cif_name = "D:\\projects\\easyScience\\easyDiffractionLib\\examples\\PDF\\Ni.cif"
-phase_cif_name = "Ni.cif"
-phases = Phases.from_cif_file(phase_cif_name)
+data_fname = r"C:\projects\easy\test\EasyDiffractionLib\examples_old\PDF2\Ni-xray.gr"
+job.add_experiment_from_file(data_fname)
 
-parameters = PDFParameters()
+phase_cif_name = r"C:\projects\easy\test\EasyDiffractionLib\examples_old\PDF2\\Ni.cif"
+job.add_sample_from_file(phase_cif_name)
 
-calculator = Calculator()
-calculator.switch("Pdffit2")
-
-job = Powder1DCW('Ni', parameters=parameters, phases=phases, interface=calculator)
-
-fitter = Fitter(job, calculator.fit_func)
 
 parameters = job.parameters
 # initial values to not be too far from optimized ones
@@ -44,8 +31,6 @@
 job.phases[0].scale = 0.366013
 job.phases[0].cell.length_a = 3.52
 
-x_data = data[:, 0]
-
 # define params to optimize
 job.phases[0].cell.length_a.fixed = False
 job.phases[0].scale.fixed = False
@@ -58,20 +43,23 @@
 
 fit_parameters = job.get_fit_parameters()
 
-result = fitter.fit(x_data, data[:, 1], 
-                    method='least_squares', minimizer_kwargs={'diff_step': 1e-5})
+calc_y_pdffit = job.calculate_profile()
+
+job.fit()
+
 
-print("The fit has been successful: {}".format(result.success))  
-print("The gooodness of fit (chi2) is: {}".format(result.reduced_chi))
+print("The fit has been successful: {}".format(job.fitting_results.success))  
+print("The gooodness of fit (chi2) is: {}".format(job.fitting_results.reduced_chi))
 
 print("The optimized parameters are:")
 for param in fit_parameters:
     print("{}: {}".format(param.name, param.raw_value))
 
-y_data = calculator.fit_func(x_data)
+y_data = job.calculate_profile()
 
 # obtain data from PdfFit calculator object
-Gobs = data[:, 1]
+x_data = job.experiment.x
+Gobs = job.experiment.y
 Gfit = y_data
 Gdiff = Gobs - Gfit
 Gdiff_baseline = -10