EasyScience · andped10 · Nov 21, 2024 · Nov 15, 2024 · Nov 15, 2024 · Nov 15, 2024
diff --git a/pyproject.toml b/pyproject.toml
@@ -34,7 +34,8 @@ dependencies = [
     "refnx>=0.1.15",
     "refl1d>=0.8.14",
     "orsopy>=0.0.4",
-    "pint==0.23"  # Only to ensure that unit is reported as dimensionless rather than empty string
+    "pint==0.23", # Only to ensure that unit is reported as dimensionless rather than empty string
+    "xhtml2pdf>=0.2.16"
 ]
 
 [project.optional-dependencies]

diff --git a/src/easyreflectometry/project.py b/src/easyreflectometry/project.py
@@ -320,10 +320,8 @@ def remove_material(self, index: int) -> None:
 
     def _default_info(self):
         return dict(
-            name='ExampleProject',
+            name='DefaultEasyReflectometryProject',
             short_description='Reflectometry, 1D',
-            samples='None',
-            experiments='None',
             modified=datetime.datetime.now().strftime('%d.%m.%Y %H:%M'),
         )
 

diff --git a/src/easyreflectometry/summary/__init__.py b/src/easyreflectometry/summary/__init__.py
@@ -0,0 +1,3 @@
+from .summary import Summary
+
+__all__ = [Summary]
diff --git a/src/easyreflectometry/summary/html_templates.py b/src/easyreflectometry/summary/html_templates.py
@@ -0,0 +1,149 @@
+HTML_TEMPLATE = """<!DOCTYPE html>
+
+<html>
+
+    <style>
+        th, td {
+            padding-right: 18px;
+        }
+        th {
+            text-align: left;
+        }
+    </style>
+
+    <body>
+        <table>
+
+            <!-- Summary title -->
+            <tr>
+                <td><h1>Summary</h1></td>
+            </tr>
+
+            <!-- Project -->
+            project_information_section
+
+            <tr></tr>
+
+            <!-- Sample -->
+            <tr>
+                <td><h2>Sample</h2></td>
+            </tr>
+            sample_section
+
+            <tr></tr>
+
+            <!-- Experiments -->
+            <tr>
+                <td><h2>Experiments</h2></td>
+            </tr>
+            experiments_section
+
+            <tr></tr>
+
+            <!-- Analysis -->
+            <tr>
+                <td><h2>Refinement</h2></td>
+            </tr>
+            refinement_section
+
+        </table>
+
+        figures_section
+
+    </body>
+</html>"""
+
+
+HTML_PROJECT_INFORMATION_TEMPLATE = """
+<tr>
+    <td><h3>Project information</h3></td>
+</tr>
+
+<tr>
+    <th>Title</th>
+    <th>project_title</th>
+</tr>
+<tr>
+    <td>Description</td>
+    <td>project_description</td>
+</tr>
+<tr>
+    <td>No. of experiments</td>
+    <td>num_experiments</td>
+</tr>
+"""
+
+HTML_PARAMETER_HEADER_TEMPLATE = """
+<tr>
+    <th>parameter_name</th> 
+    <th>parameter_value</th>
+    <th>parameter_unit</th> 
+    <th>parameter_error</th>
+</tr>
+"""
+
+HTML_PARAMETER_TEMPLATE = """
+<tr>
+    <td>parameter_name</td> 
+    <td>parameter_value</td>
+    <td>parameter_unit</td> 
+    <td>parameter_error</td>
+</tr>
+"""
+
+HTML_DATA_COLLECTION_TEMPLATE = """
+<tr>
+    <th>Experiment datablock</th>
+    <th>experiment_name</th>
+</tr>
+<tr>
+    <td>Measured intensity range:</td>
+    <td>[range_min, range_max]</td>
+</tr>
+<tr>
+    <td>No. of data points</td>
+    <td>num_data_points</td>
+</tr>
+<tr>
+    <td>Resolution function</td>
+    <td>resolution_function</td>
+</tr>
+
+"""
+
+HTML_REFINEMENT_TEMPLATE = """
+<tr>
+    <td>Calculation engine</td>
+    <td>calculation_engine</td>
+</tr>
+<tr>
+    <td>Minimization engine</td>
+    <td>minimization_engine</td>
+</tr>
+<!-- <tr> -->
+<!--     <td>Goodness-of-fit: reduced <i>&chi;</i><sup>2</sup></td> -->
+<!--     <td>goodness_of_fit</td> -->
+<!-- </tr> -->
+<tr>
+    <td>No. of parameters:</td>
+    <td>num_total_params</td>
+</tr>
+<tr>
+    <td>No. of free parameters:</td>
+    <td>num_free_params</td>
+</tr>
+<tr>
+    <td>No. of fixed parameters:</td>
+    <td>num_fixed_params</td>
+</tr>
+<tr>
+    <td>No. of constraints</td>
+    <td>num_constriants</td>
+</tr>
+"""
+
+HTML_FIGURES_TEMPLATE = """
+<img src="path_sld_plot" alt="SLD plot" width="640" height="480">
+<br>
+<img src="path_fit_experiment_plot" alt="Fit experiment plot" width="640" height="480">
+"""
diff --git a/src/easyreflectometry/summary/summary.py b/src/easyreflectometry/summary/summary.py
@@ -0,0 +1,189 @@
+import matplotlib.pyplot as plt
+import numpy as np
+from easyscience import global_object
+from xhtml2pdf import pisa
+
+from easyreflectometry import Project
+from easyreflectometry.utils import count_fixed_parameters
+from easyreflectometry.utils import count_free_parameters
+from easyreflectometry.utils import count_parameter_user_constraints
+
+from .html_templates import HTML_DATA_COLLECTION_TEMPLATE
+from .html_templates import HTML_FIGURES_TEMPLATE
+from .html_templates import HTML_PARAMETER_HEADER_TEMPLATE
+from .html_templates import HTML_PARAMETER_TEMPLATE
+from .html_templates import HTML_PROJECT_INFORMATION_TEMPLATE
+from .html_templates import HTML_REFINEMENT_TEMPLATE
+from .html_templates import HTML_TEMPLATE
+
+
+class Summary:
+    def __init__(self, project: Project):
+        self._project = project
+
+    def compile_html_summary(self, figures: bool = False) -> str:
+        html = HTML_TEMPLATE
+        project_information_section = self._project_information_section()
+        if project_information_section == '':  # no project information
+            project_information_section = '<td>No project information</td>'
+        html = html.replace('project_information_section', project_information_section)
+
+        html = html.replace('sample_section', self._sample_section())
+
+        experiments_section = self._experiments_section()
+        if experiments_section == '':  # no experiments
+            experiments_section = '<td>No experiments</td>'
+        html = html.replace('experiments_section', experiments_section)
+
+        html = html.replace('refinement_section', self._refinement_section())
+
+        if figures:
+            html = html.replace('figures_section', self._figures_section())
+        else:
+            html = html.replace('figures_section', '')
+
+        return html
+
+    def save_html_summary(self, filename: str) -> None:
+        html = self.compile_html_summary(figures=True)
+        with open(filename, 'w') as f:
+            f.write(html)
+
+    def save_pdf_summary(self, filename: str) -> None:
+        html = self.compile_html_summary(figures=True)
+
+        with open(filename, 'w+b') as result_file:
+            pisa_status = pisa.CreatePDF(
+                html,
+                dest=result_file,
+            )
+
+            if pisa_status.err:
+                print('An error occured when generating PDF summary!')
+
+    def save_sld_plot(self, filename: str) -> None:
+        fig = plt.figure()
+        ax = fig.add_subplot(1, 1, 1)
+
+        sld = self._project.sld_data_for_model_at_index(0)
+        ax.plot(sld.x, sld.y)
+
+        ax.set_xlabel('z (Å)')
+        ax.set_ylabel('SLD (Å⁻²)')
+        fig.savefig(filename, dpi=300)
+        plt.close()
+
+    def save_fit_experiment_plot(self, filename: str) -> None:
+        fig = plt.figure()
+        ax = fig.add_subplot(1, 1, 1)
+
+        model = self._project.model_data_for_model_at_index(0)
+        ax.plot(model.x, np.log10(model.y), color='blue')
+
+        try:
+            experiment = self._project.experimental_data_for_model_at_index(0)
+            ax.plot(experiment.x, np.log10(experiment.y), color='red')
+        except IndexError:
+            pass
+
+        ax.set_xlabel('Q (Å⁻¹)')
+        ax.set_ylabel('Reflectivity')
+        fig.savefig(filename, dpi=300)
+        plt.close()
+
+    def _project_information_section(self) -> str:
+        html_project = ''
+        if self._project.created:
+            html_project = HTML_PROJECT_INFORMATION_TEMPLATE
+            name = self._project._info['name']
+            short_description = self._project._info['short_description']
+            html_project = html_project.replace('project_title', f'{name}')
+            html_project = html_project.replace('project_description', f'{short_description}')
+            html_project = html_project.replace('num_experiments', f'{len(self._project.experiments)}')
+        return html_project
+
+    def _sample_section(self) -> str:
+        html_parameters = []
+
+        html_parameter = HTML_PARAMETER_HEADER_TEMPLATE
+        html_parameter = html_parameter.replace('parameter_name', 'Name')
+        html_parameter = html_parameter.replace('parameter_value', 'Value')
+        html_parameter = html_parameter.replace('parameter_unit', 'Unit')
+        html_parameter = html_parameter.replace('parameter_error', 'Error')
+        html_parameters.append(html_parameter)
+
+        for parameter in self._project.parameters:
+            path = global_object.map.find_path(
+                self._project._models[self._project.current_model_index].unique_name, parameter.unique_name
+            )
+            if 0 < len(path):
+                name = f'{global_object.map.get_item_by_key(path[-2]).name} {global_object.map.get_item_by_key(path[-1]).name}'
+            else:
+                name = parameter.name
+            value = parameter.value
+            unit = parameter.unit
+            error = parameter.error
+
+            html_parameter = HTML_PARAMETER_TEMPLATE
+            html_parameter = html_parameter.replace('parameter_name', f'{name}')
+            html_parameter = html_parameter.replace('parameter_value', f'{value}')
+            html_parameter = html_parameter.replace('parameter_unit', f'{unit}')
+            html_parameter = html_parameter.replace('parameter_error', f'{error}')
+            html_parameters.append(html_parameter)
+
+        html_parameters_str = '\n'.join(html_parameters)
+
+        return html_parameters_str
+
+    def _experiments_section(self) -> str:
+        html_experiments = []
+
+        for idx, experiment in self._project.experiments.items():
+            experiment_name = experiment.name
+            num_data_points = len(experiment.x)
+            resolution_function = self._project.models[idx].resolution_function.as_dict()['smearing']
+            if resolution_function == 'PercentageFhwm':
+                precentage = self._project.models[idx].resolution_function.as_dict()['constant']
+                resolution_function = f'{resolution_function} {precentage}%'
+            range_min = min(experiment.y)
+            range_max = max(experiment.y)
+            range_units = 'Å⁻¹'
+            html_experiment = HTML_DATA_COLLECTION_TEMPLATE
+            html_experiment = html_experiment.replace('experiment_name', f'{experiment_name}')
+            html_experiment = html_experiment.replace('range_min', f'{range_min}')
+            html_experiment = html_experiment.replace('range_max', f'{range_max}')
+            html_experiment = html_experiment.replace('range_units', f'{range_units}')
+            html_experiment = html_experiment.replace('num_data_points', f'{num_data_points}')
+            html_experiment = html_experiment.replace('resolution_function', f'{resolution_function}')
+            html_experiments.append(html_experiment)
+
+        html_experiments_str = '\n'.join(html_experiments)
+
+        return html_experiments_str
+
+    def _refinement_section(self) -> str:
+        html_refinement = HTML_REFINEMENT_TEMPLATE
+        num_free_params = count_free_parameters(self._project)
+        num_fixed_params = count_fixed_parameters(self._project)
+        num_params = num_free_params + num_fixed_params
+        #        goodness_of_fit = self._project.status.goodnessOfFit
+        #        goodness_of_fit = goodness_of_fit.split(' → ')[-1]
+        num_constraints = count_parameter_user_constraints(self._project)
+
+        html_refinement = html_refinement.replace('calculation_engine', f'{self._project._calculator.current_interface_name}')
+        html_refinement = html_refinement.replace('minimization_engine', f'{self._project.minimizer.name}')
+        #        html = html.replace('goodness_of_fit', f'{goodness_of_fit}')
+        html_refinement = html_refinement.replace('num_total_params', f'{num_params}')
+        html_refinement = html_refinement.replace('num_free_params', f'{num_free_params}')
+        html_refinement = html_refinement.replace('num_fixed_params', f'{num_fixed_params}')
+        html_refinement = html_refinement.replace('num_constriants', f'{num_constraints}')
+        return html_refinement
+
+    def _figures_section(self) -> None:
+        html_figures = HTML_FIGURES_TEMPLATE
+        self.save_sld_plot(self._project.path / 'sld_plot.jpg')
+        self.save_fit_experiment_plot(self._project.path / 'fit_experiment_plot.jpg')
+
+        html_figures = html_figures.replace('path_sld_plot', str(self._project.path / 'sld_plot.jpg'))
+        html_figures = html_figures.replace('path_fit_experiment_plot', str(self._project.path / 'fit_experiment_plot.jpg'))
+        return html_figures
diff --git a/src/easyreflectometry/utils.py b/src/easyreflectometry/utils.py
@@ -71,3 +71,29 @@ def collect_unique_names_from_dict(structure_dict: dict, unique_names: Optional[
             if key == 'unique_name':
                 unique_names.append(value)
     return unique_names
+
+
+def count_free_parameters(project) -> int:
+    count = 0
+    parameters = project.parameters
+    for parameter in parameters:
+        if parameter.free:
+            count = count + 1
+    return count
+
+
+def count_fixed_parameters(project) -> int:
+    count = 0
+    parameters = project.parameters
+    for parameter in parameters:
+        if not parameter.free:
+            count = count + 1
+    return count
+
+
+def count_parameter_user_constraints(project) -> int:
+    count = 0
+    parameters = project.parameters
+    for parameter in parameters:
+        count = count + len(parameter.user_constraints.keys())
+    return count