Merge pull request #148 from EasyScience/develop

Release 0.1.5

Author: AndrewSazonov

.github/workflows/release-drafter.yml

@@ -16,3 +16,21 @@ jobs:
       - uses: release-drafter/release-drafter@v6
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Check-out repository
+        uses: actions/checkout@v4
+
+      # Zips the examples directory
+      - name: Zip examples directory
+        run: zip -r examples.zip examples/
+
+      # Uploads the zipped examples directory to the release draft
+      - name: Upload zipped examples directory
+        uses: actions/upload-release-asset@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          upload_url: ${{ steps.create_release.outputs.upload_url }} # This pulls from the create_release step above
+          asset_path: ./examples.zip
+          asset_name: examples.zip
+          asset_content_type: application/zip

.github/workflows/test-ipynb.yml

@@ -86,7 +86,8 @@ jobs:
         shell: bash
         run: >
           pytest 
-          --nbmake examples/*ipynb 
+          --nbmake examples 
+          --ignore-glob='examples/*emcee*'
           --nbmake-timeout=300 
           --color=yes
           -n=auto

.github/workflows/test-package.yaml

@@ -117,7 +117,8 @@ jobs:
       shell: bash
       run: >
         pytest 
-        --nbmake examples/*ipynb 
+        --nbmake examples 
+        --ignore-glob='examples/*emcee*'
         --nbmake-timeout=300 
         --color=yes
         -n=auto  

easydiffraction/Job.py

@@ -140,6 +140,7 @@ def __init__(
         self.sample = sample # container for phases
         self.interface = self.sample._interface
         self.analysis = analysis
+        self.update_job_type()
         # necessary for the fitter
         # TODO: remove the dependency on kwargs
         self._kwargs = {}
@@ -329,7 +330,14 @@ def update_job_type(self) -> None:
         self.type.is_tof = self.experiment.is_tof
         self.type.is_sc = self.experiment.is_single_crystal
         self.type.is_2d = self.experiment.is_2d
-
+        # radiation
+        if hasattr(self.sample, 'pattern') and self.sample.pattern is not None:
+            if self.type.is_xray:
+                self.sample.pattern.radiation = "x-ray"
+            elif self.type.is_neut:
+                self.sample.pattern.radiation = "neutron"
+
+        # axis
         if self.type.is_tof:
             self._x_axis_name = "time"
             if self.pattern is not None:
@@ -587,16 +595,27 @@ def fit(self, **kwargs):
         if result is None:
             raise ValueError("Fitting failed")
 
+        # Print fitting result. If in a notebook, use emojis.
+        success_msg = "Success"
+        failure_msg = "Failure"
+        duration_msg = f"{end - start:.2f} s"
+        if self.is_notebook():
+            success_msg = f'🥳 {success_msg}'
+            failure_msg = f'😩 {failure_msg}'
+            duration_msg = f'⌛ {duration_msg}'
+        print("Fitting result")
         if result.success:
-            print("Fitting successful")
-            print(f"Duration: {end - start:.2f} s")
-            print(f"Reduced chi: {result.reduced_chi:.2f}")
+            reduced_chi_msg = f"{result.reduced_chi:.2f}"
+            if self.is_notebook():
+                reduced_chi_msg = f'👍 {reduced_chi_msg}'
+            print(f'Status: {success_msg}')
+            print(f'Duration: {duration_msg}')
+            print(f'Reduced χ²: {reduced_chi_msg}')
         else:
-            print("Fitting failed.")
+            print(f'Status: {failure_msg}')
 
         self.fitting_results = result
 
-
     ###### UTILITY METHODS ######
     def add_datastore(self, datastore: xr.Dataset):
         '''
@@ -632,16 +651,16 @@ def show_crystal_structure(self, id=None):
         phase = self.phases[id]
         cif = phase.cif
 
-        structure_view = py3Dmol.view(linked=False)
+        structure_view = py3Dmol.view(width=540, height=480, linked=False)
         structure_view.addModel(cif, 'cif')
         structure_view.setStyle({'sphere': {'colorscheme': 'Jmol', 'scale': .2},
                                  'stick': {'colorscheme': 'Jmol', 'radius': 0.1}})
         if importlib.util.find_spec("darkdetect") is not None and darkdetect.isDark():
             structure_view.setBackgroundColor('#111')
         structure_view.addUnitCell()
         structure_view.replicateUnitCell(2, 2, 2)
-        structure_view.zoomTo()
-        structure_view.show()
+        structure_view.zoomTo()  # To zoom in to the center of the structure
+        structure_view.show()  # To display the contents of the view object on Jupyter notebook.
 
     def print_data(self):
         '''
@@ -728,6 +747,62 @@ def show_experiment_chart(self, show_legend=True):
 
         fig.show()
 
+    def show_simulation_chart(self, show_legend=True):
+        '''
+        Show the simulation chart.
+        '''
+        if importlib.util.find_spec("plotly") is None:
+            print("Warning: Plotly not installed. Try `pip install plotly`.")
+            return
+
+        if self.type.is_pd and self.type.is_cwl:
+            x_axis_title = '2θ (degree)'
+            x = np.arange(self.instrument.twotheta_range_min.raw_value,
+                          self.instrument.twotheta_range_max.raw_value + self.instrument.twotheta_range_inc.raw_value,
+                          self.instrument.twotheta_range_inc.raw_value)
+        elif self.type.is_pd and self.type.is_tof:
+            x_axis_title = 'TOF (µs)'
+            x = np.arange(self.instrument.tof_range_min.raw_value,
+                          self.instrument.tof_range_max.raw_value + self.instrument.tof_range_inc.raw_value,
+                          self.instrument.tof_range_inc.raw_value)
+        else:
+            print(f"Warning: Simulation chart not available for this type of job '{self.type}'")
+            print("Supported types: 'pd-cwl' and 'pd-tof'")
+
+        y_calc = self.calculate_profile(x)
+
+        main_y_range = y_calc.max() - y_calc.min()
+        main_y_min = y_calc.min() - main_y_range / 10
+        main_y_max = y_calc.max() + main_y_range / 10
+
+        trace_calc = go.Scatter(
+            x=x,
+            y=y_calc,
+            line=dict(color='rgb(214, 39, 40)'),
+            mode='lines',
+            name='Total calculated (Icalc)'
+        )
+
+        data = [trace_calc]
+
+        layout = go.Layout(
+            autosize=True,
+            margin=dict(autoexpand=True,
+                        r=30, t=30, b=45),
+            legend=dict(yanchor="top", y=1.0,
+                        xanchor="right", x=1.0),
+            xaxis=dict(title_text=x_axis_title),
+            yaxis=dict(title_text='Icalc', range=[main_y_min, main_y_max]),
+        )
+
+        fig = go.Figure(data=data, layout=layout)
+
+        fig.update_xaxes(showline=True, mirror=True, zeroline=False)
+        fig.update_yaxes(showline=True, mirror=True, zeroline=False)
+        fig.update_layout(showlegend=show_legend)
+
+        fig.show()
+
     def show_analysis_chart(self, show_legend=True):
         '''
         Show the analysis chart.

easydiffraction/Profiles/P1D.py

@@ -14,6 +14,7 @@
 
 from easyscience.Datasets.xarray import xr
 from easyscience.Objects.ObjectClasses import BaseObj
+from easyscience.Objects.ObjectClasses import Descriptor
 from easyscience.Objects.ObjectClasses import Parameter
 
 from easydiffraction.components.polarization import PolarizedBeam
@@ -244,6 +245,48 @@ class Instrument1DCWParameters(BaseObj):
             "url": "https://docs.easydiffraction.org/lib/project/dictionaries/_pd_instr/",
             "value": 0.0,
             "fixed": True,
+        },
+        "twotheta_range_min": {
+            "name": "twotheta_range_min",
+            "url": "https://docs.easydiffraction.org/lib/project/dictionaries/_pd_meas/",
+            "value": 10.0,
+            "fixed": True,
+            "enabled": False,
+        },
+        "twotheta_range_max": {
+            "name": "twotheta_range_max",
+            "url": "https://docs.easydiffraction.org/lib/project/dictionaries/_pd_meas/",
+            "value": 170.0,
+            "fixed": True,
+            "enabled": False,
+        },
+        "twotheta_range_inc": {
+            "name": "twotheta_range_inc",
+            "url": "https://docs.easydiffraction.org/lib/project/dictionaries/_pd_meas/",
+            "value": 0.1,
+            "fixed": True,
+            "enabled": False,
+        },
+        "tof_range_min": {
+            "name": "tof_range_min",
+            "url": "https://docs.easydiffraction.org/lib/project/dictionaries/_pd_meas/",
+            "value": 10000.0,
+            "fixed": True,
+            "enabled": False,
+        },
+        "tof_range_max": {
+            "name": "tof_range_max",
+            "url": "https://docs.easydiffraction.org/lib/project/dictionaries/_pd_meas/",
+            "value": 100000.0,
+            "fixed": True,
+            "enabled": False,
+        },
+        "tof_range_inc": {
+            "name": "tof_range_inc",
+            "url": "https://docs.easydiffraction.org/lib/project/dictionaries/_pd_meas/",
+            "value": 5.0,
+            "fixed": True,
+            "enabled": False,
         }
     }
 
@@ -257,6 +300,12 @@ class Instrument1DCWParameters(BaseObj):
     reflex_asymmetry_p2: ClassVar[Parameter]
     reflex_asymmetry_p3: ClassVar[Parameter]
     reflex_asymmetry_p4: ClassVar[Parameter]
+    twotheta_range_min: ClassVar[Descriptor]
+    twotheta_range_max: ClassVar[Descriptor]
+    twotheta_range_inc: ClassVar[Descriptor]
+    tof_range_min: ClassVar[Descriptor]
+    tof_range_max: ClassVar[Descriptor]
+    tof_range_inc: ClassVar[Descriptor]
 
     def __init__(
         self,
@@ -270,6 +319,12 @@ def __init__(
         reflex_asymmetry_p2: Optional[Union[Parameter, float]] = None,
         reflex_asymmetry_p3: Optional[Union[Parameter, float]] = None,
         reflex_asymmetry_p4: Optional[Union[Parameter, float]] = None,
+        twotheta_range_min: Optional[Union[Descriptor, float]] = None,
+        twotheta_range_max: Optional[Union[Descriptor, float]] = None,
+        twotheta_range_inc: Optional[Union[Descriptor, float]] = None,
+        tof_range_min: Optional[Union[Descriptor, float]] = None,
+        tof_range_max: Optional[Union[Descriptor, float]] = None,
+        tof_range_inc: Optional[Union[Descriptor, float]] = None,
         interface: Optional[iF] = None,
     ):
         super(Instrument1DCWParameters, self).__init__(
@@ -299,6 +354,18 @@ def __init__(
             self.reflex_asymmetry_p3 = reflex_asymmetry_p3
         if reflex_asymmetry_p4 is not None:
             self.reflex_asymmetry_p4 = reflex_asymmetry_p4
+        if twotheta_range_min is not None:
+            self.twotheta_range_min = twotheta_range_min
+        if twotheta_range_max is not None:
+            self.twotheta_range_max = twotheta_range_max
+        if twotheta_range_inc is not None:
+            self.twotheta_range_inc = twotheta_range_inc
+        if tof_range_min is not None:
+            self.tof_range_min = tof_range_min
+        if tof_range_max is not None:
+            self.tof_range_max = tof_range_max
+        if tof_range_inc is not None:
+            self.tof_range_inc = tof_range_inc
         self.name = self._name
         self.interface = interface
 

easydiffraction/__init__.py

@@ -9,6 +9,7 @@
 from .components.phase import Phases as Phases
 from .components.site import Atoms as Atoms
 from .components.site import Site as Site
+from .io.download import download_from_repository
 from .Job import DiffractionJob as Job
 
-__all__ = ['Job']
+__all__ = ['Job', 'download_from_repository']

easydiffraction/io/download.py

@@ -0,0 +1,24 @@
+# SPDX-FileCopyrightText: 2024 EasyDiffraction contributors
+# SPDX-License-Identifier: BSD-3-Clause
+# © 2021-2024 Contributors to the EasyDiffraction project <https://github.com/easyscience/EasyDiffraction
+
+import pooch
+
+
+def download_from_repository(fname : str, branch : str = 'master', destination : str = 'data'):
+    '''
+    This function downloads a file from the EasyDiffraction repository on GitHub.
+    :param fname: The name of the file to download
+    :param destination: The destination folder to save the file
+    :return: None
+    '''
+    organisation = 'EasyScience'
+    repository = 'EasyDiffractionLib'
+    source = 'examples/data'
+    url = f'https://raw.githubusercontent.com/{organisation}/{repository}/refs/heads/{branch}/{source}/{fname}'
+    pooch.retrieve(
+        url=url,
+        known_hash=None,
+        fname=fname,
+        path=destination,
+    )