initial work on full tof support in EDA.

src/easydiffraction/io/cif.py

@@ -15,6 +15,7 @@
 from typing import Tuple
 from typing import Union
 
+import numpy as np
 from easycrystallography.Components.AtomicDisplacement import AtomicDisplacement
 from easycrystallography.Components.Lattice import Lattice
 from easycrystallography.Components.SpaceGroup import SpaceGroup
@@ -1050,9 +1051,51 @@ def str2float(text):
             return 0
         raise ex
 
-
 def dataBlockToCif(block, includeBlockName=True):
     cif = ''
+
+    if includeBlockName:
+        cif += f"data_{block['name']['value']}"
+        cif += '\n\n'
+
+    if 'params' in block:
+        for category in block['params'].values():
+            for param in category.values():
+                # if param["optional"]:
+                #     continue
+
+                value = param["value"]
+                if value is None:
+                    continue
+
+                if isinstance(value, (float, int)):  # If parameter is of float type
+                    value = np.float32(value)  # Simplifies output
+                    if param["fit"]:
+                        error = param["error"]
+                        #error = np.float32(error)  # Simplifies output
+                        if error == 0:
+                            paramStr = f'{value}()' # Adds empty brackets for standard uncertainty for free params
+                        else:
+                            _, _, paramStr = IO.toStdDevSmalestPrecision(value, error) # Adds brackets with standard uncertainty for free params
+                    else:
+                        paramStr = str(value)  # Keeps 32bit presicion format in contrast to f'{...}'
+                elif isinstance(value, str):  # If parameter is of string type
+                    if ' ' in value:  # Adds quotes to text with spaces, e.g. P n m a -> "P n m a"
+                        paramStr = f'"{value}"'
+                    else:
+                        paramStr = f'{value}'
+                else:
+                    console.error(f'Unsupported parameter type {type(value)} for {value}')
+                    continue
+
+                cif += f'{param["category"]}.{param["name"]} {paramStr}'
+                cif += '\n'
+            cif += '\n'
+    return cif
+
+
+def dataBlockToCif_old(block, includeBlockName=True):
+    cif = ''
     if includeBlockName:
         cif += f'data_{block["name"]["value"]}'
         cif += '\n\n'

src/easydiffraction/io/cif_reader.py

@@ -145,10 +145,17 @@ def parameters_from_cif_block(block) -> dict:
     if value is not None:
         parameters['dtt2'] = {}
         parameters['dtt2']['value'], parameters['dtt2']['error'] = parse_with_error(value)
+
     value = block.find_value('_pd_instr_2theta_bank') or block.find_value('_pd_instr.2theta_bank')
     if value is not None:
         parameters['2theta_bank'] = {}
         parameters['2theta_bank']['value'], parameters['2theta_bank']['error'] = parse_with_error(value)
+
+    value = block.find_value('_pd_instr.zero') or block.find_value('_pd_instr_zero')
+    if value is not None:
+        parameters['zero'] = {}
+        parameters['zero']['value'], parameters['zero']['error'] = parse_with_error(value)
+
     value = block.find_value('_pd_instr_peak_shape') or block.find_value('_pd_instr.peak_shape')
     if value is not None:
         parameters['peak_shape'] = value

src/easydiffraction/job/experiment/experiment.py

@@ -249,6 +249,11 @@ def tof_parameters_from_dict(self, p: dict):
             if p['2theta_bank'].get('error') is not None:
                 parameters.ttheta_bank.error = p['2theta_bank'].get('error')
                 parameters.ttheta_bank.fixed = False
+        if 'zero' in p:
+            parameters.zero = p['zero'].get('value', 0.0)
+            if p['zero'].get('error') is not None:
+                parameters.zero.error = p['zero'].get('error')
+                parameters.zero.fixed = False
         if 'alpha0' in p:
             parameters.alpha0 = p['alpha0'].get('value', 0.0)
             if p['alpha0'].get('error') is not None:

src/easydiffraction/job/experiment/pd_1d.py

@@ -461,6 +461,12 @@ class Instrument1DTOFParameters(BaseObj):
             'value': 0.00224,
             'fixed': True,
         },
+        'zero': {
+            'name': 'zero',
+            'url': 'https://docs.easydiffraction.org/lib/dictionaries/_pd_instr/',
+            'value': 0.0,
+            'fixed': True,
+        },
     }
 
     ttheta_bank: ClassVar[Parameter]
@@ -476,6 +482,7 @@ class Instrument1DTOFParameters(BaseObj):
     alpha1: ClassVar[Parameter]
     beta0: ClassVar[Parameter]
     beta1: ClassVar[Parameter]
+    zero: ClassVar[Parameter]
 
     def __init__(
         self,
@@ -492,6 +499,7 @@ def __init__(
         alpha1: Optional[Union[Parameter, float]] = None,
         beta0: Optional[Union[Parameter, float]] = None,
         beta1: Optional[Union[Parameter, float]] = None,
+        zero: Optional[Union[Parameter, float]] = None,
         interface: Optional[iF] = None,
     ):
         super().__init__(
@@ -525,6 +533,8 @@ def __init__(
             self.beta0 = beta0
         if beta1 is not None:
             self.beta1 = beta1
+        if zero is not None:
+            self.zero = zero
 
         self.name = self._name
         self.interface = interface

src/easydiffraction/job/job.py

@@ -420,7 +420,11 @@ def add_experiment_from_file(self, file_url: str) -> None:
             self.experiment.from_xye_file(file_url)
         else:
             self.experiment.from_cif_file(file_url)
+        self.update_after_new_experiment()
 
+    def update_after_new_experiment(self) -> None:
+        """
+        """
         self.update_experiment_type()
         # re-do the sample in case of type change.
         # Different type read in (likely TOF), so re-create the sample
@@ -453,7 +457,7 @@ def add_experiment_from_string(self, cif_string: str) -> None:
         Just a wrapper around the Experiment class method.
         """
         self.experiment.from_cif_string(cif_string)
-        self.update_experiment_type()
+        self.update_after_new_experiment()
 
     def add_sample_from_file(self, file_url: str) -> None:
         """