No dynamic classes (#2)

* Refactor peak asymmetry classes and improve docs

* Refactor peak broadening handling with a factory

* Enhance Descriptor class with new attributes

* Refactor type hints for clarity

* Update peak broadening parameters and descriptions

* Refactor parameter initialization for clarity

* Create class Peak

* New implementation with dynamically attached attributes

* Refactor experiment imports and add convenience API

* Fix advanced example

* Refine strategy descriptions and cleanup code

* Refactor background handling and add new types

* Add CIF analysis display feature

* Update descriptions for clarity and detail

* Clean up

* Add item access and iteration methods

* Clean up

* Improve project loading and saving functionality

* Update project save path for clarity

* Clean up

* Refactor component base and instrument classes

* Clean up

* Refactor attribute formatting and rename files

* Refactor components for better parameter handling

* New peak.py

* Refactor peak profile handling

* Refactors component architecture for iterables

* Refactors CIF category definition for components

* Adds generic `as_dict` method to ComponentBase

* Refactors core component structure

* Renames "refinement" to "fitting" for clarity.

Author: AndrewSazonov

README.md

@@ -25,6 +25,7 @@ Development playground for the new EasyDiffraction API.
   ```
 
 ## Testing
+
   ```bash
   PYTHONPATH=$(pwd)/src python -m pytest tests/ --color=yes
   ```
@@ -33,9 +34,9 @@ Development playground for the new EasyDiffraction API.
 
 - Simplified API:
   ```bash
-  PYTHONPATH=$(pwd)/src python examples/joint-refinement_simple-api.py
+  PYTHONPATH=$(pwd)/src python examples/joint-fit_simple-api.py
   ```
 - Advanced API:
   ```bash
-  PYTHONPATH=$(pwd)/src python examples/joint-refinement_advanced-api.py
+  PYTHONPATH=$(pwd)/src python examples/joint-fit_advanced-api.py
   ```

examples/joint-refinement_advanced-api.py renamed to examples/joint-fit_advanced-api.py

@@ -29,14 +29,15 @@
 
 # Experiment 1: Neutron powder diffraction
 expt1 = Experiment(id="npd", radiation_probe="neutron", data_path="examples/data/pbso4_powder_neutron_cw.dat")
-expt1.instr_setup.wavelength = 1.91
-expt1.instr_calib.twotheta_offset = -0.1406
-expt1.peak_broad.gauss_u = 0.139
-expt1.peak_broad.gauss_v = -0.412
-expt1.peak_broad.gauss_w = 0.386
-expt1.peak_broad.lorentz_x = 0
-expt1.peak_broad.lorentz_y = 0.088
+expt1.instrument.setup_wavelength = 1.91
+expt1.instrument.calib_twotheta_offset = -0.1406
+expt1.peak.broad_gauss_u = 0.139
+expt1.peak.broad_gauss_v = -0.412
+expt1.peak.broad_gauss_w = 0.386
+expt1.peak.broad_lorentz_x = 0
+expt1.peak.broad_lorentz_y = 0.088
 expt1.linked_phases.add("pbso4", scale=1.0)
+expt1.background_type = "line-segment"
 for x, y in [
     (11.0, 206.1624),
     (15.0, 194.75),
@@ -51,23 +52,22 @@
 
 # Experiment 2: X-ray powder diffraction
 expt2 = Experiment(id="xrd", radiation_probe="xray", data_path="examples/data/pbso4_powder_xray.dat")
-expt2.instr_setup.wavelength = 1.540567
-expt2.instr_calib.twotheta_offset = -0.05181
-expt2.peak_broad.gauss_u = 0.304138
-expt2.peak_broad.gauss_v = -0.112622
-expt2.peak_broad.gauss_w = 0.021272
-expt2.peak_broad.lorentz_x = 0
-expt2.peak_broad.lorentz_y = 0.057691
+expt2.instrument.setup_wavelength = 1.540567
+expt2.instrument.calib_twotheta_offset = -0.05181
+expt2.peak.broad_gauss_u = 0.304138
+expt2.peak.broad_gauss_v = -0.112622
+expt2.peak.broad_gauss_w = 0.021272
+expt2.peak.broad_lorentz_x = 0
+expt2.peak.broad_lorentz_y = 0.057691
 expt2.linked_phases.add("pbso4", scale=0.005)
+expt2.background_type = "chebyshev polynomial"
 for x, y in [
-    (11.0, 141.8516),
-    (13.0, 102.8838),
-    (16.0, 78.0551),
-    (20.0, 124.0121),
-    (30.0, 123.7123),
-    (50.0, 120.8266),
-    (90.0, 113.7473),
-    (110.0, 132.4643),
+    (0, 119.195),
+    (1, 6.221),
+    (2, -45.725),
+    (3, 8.119),
+    (4, 54.552),
+    (5, -20.661),
 ]:
     expt2.background.add(x, y)
 
@@ -80,7 +80,7 @@
 # Set calculator, minimizer and refinement strategy
 project.analysis.current_calculator = "crysfml"
 project.analysis.current_minimizer = "lmfit (leastsq)"
-project.analysis.refinement_strategy = 'combined'
+project.analysis.fit_mode = 'joint'
 
 # Define free parameters
 model.cell.length_a.free = True

examples/joint-refinement_simple-api.py renamed to examples/joint-fit_simple-api.py

@@ -32,7 +32,7 @@
 The objective is to accurately refine the crystal structure of PbSO4."""
 
 # Save the initial project specifying the directory path
-project.save_as("examples/pbso4_joint")
+project.save_as("examples/projects/pbso4_joint")
 
 # Show project metadata
 project.info.show_as_cif()
@@ -104,17 +104,14 @@
 
 print(ed.chapter('Step 3: Add Experiments (Instrument models and measured data)'))
 
-print(ed.section('Add experiments'))
-
-# Add two experiments
 project.experiments.add(id="npd",
-                        diffr_mode="powder",
-                        expt_mode="constant_wavelength",
+                        sample_form="powder",
+                        beam_mode="constant wavelength",
                         radiation_probe="neutron",
                         data_path="examples/data/pbso4_powder_neutron_cw.dat")
 project.experiments.add(id="xrd",
-                        diffr_mode="powder",
-                        expt_mode="constant_wavelength",
+                        sample_form="powder",
+                        beam_mode="constant wavelength",
                         radiation_probe="xray",
                         data_path="examples/data/pbso4_powder_xray.dat")
 
@@ -126,25 +123,31 @@
 project.experiments['xrd'].show_meas_chart(x_min=26, x_max=28)
 
 # Modify experimental parameters
-project.experiments['npd'].instr_setup.wavelength = 1.91
-project.experiments["npd"].instr_calib.twotheta_offset = -0.1406
-project.experiments["npd"].peak_broad.gauss_u = 0.139
-project.experiments["npd"].peak_broad.gauss_v = -0.412
-project.experiments["npd"].peak_broad.gauss_w = 0.386
-project.experiments["npd"].peak_broad.lorentz_x = 0
-project.experiments["npd"].peak_broad.lorentz_y = 0.088
-
-project.experiments['xrd'].instr_setup.wavelength = 1.540567
-project.experiments["xrd"].instr_calib.twotheta_offset = -0.05181
-project.experiments["xrd"].peak_broad.gauss_u = 0.304138
-project.experiments["xrd"].peak_broad.gauss_v = -0.112622
-project.experiments["xrd"].peak_broad.gauss_w = 0.021272
-project.experiments["xrd"].peak_broad.lorentz_x = 0
-project.experiments["xrd"].peak_broad.lorentz_y = 0.057691
+project.experiments['npd'].instrument.setup_wavelength = 1.91
+project.experiments["npd"].instrument.calib_twotheta_offset = -0.1406
+
+project.experiments["npd"].show_supported_peak_profile_types()
+project.experiments["npd"].peak_profile_type = "ikeda-carpenter"
+project.experiments["npd"].show_current_peak_profile_type()
+project.experiments["npd"].peak_profile_type = "split pseudo-voigt"
+project.experiments["npd"].peak_profile_type = "pseudo-voigt"
+project.experiments["npd"].peak.broad_gauss_u = 0.139
+project.experiments["npd"].peak.broad_gauss_v = -0.412
+project.experiments["npd"].peak.broad_gauss_w = 0.386
+project.experiments["npd"].peak.broad_lorentz_x = 0
+project.experiments["npd"].peak.broad_lorentz_y = 0.088
+
+project.experiments['xrd'].instrument.setup_wavelength = 1.540567
+project.experiments["xrd"].instrument.calib_twotheta_offset = -0.05181
+project.experiments["xrd"].peak.broad_gauss_u = 0.304138
+project.experiments["xrd"].peak.broad_gauss_v = -0.112622
+project.experiments["xrd"].peak.broad_gauss_w = 0.021272
+project.experiments["xrd"].peak.broad_lorentz_x = 0
+project.experiments["xrd"].peak.broad_lorentz_y = 0.057691
 
 # Link sample model to experiments
 project.experiments['npd'].linked_phases.add(id='pbso4', scale=1.0)
-project.experiments['xrd'].linked_phases.add(id='pbso4', scale=0.005)
+project.experiments['xrd'].linked_phases.add(id='pbso4', scale=0.002)
 
 # Show experiments as CIF
 project.experiments["npd"].show_as_cif()
@@ -161,7 +164,7 @@
 print(ed.chapter('Step 4: Analysis'))
 
 print(ed.section('Set calculator'))
-project.analysis.show_available_calculators()
+project.analysis.show_supported_calculators()
 project.analysis.show_current_calculator()
 project.analysis.current_calculator = 'crysfml'
 
@@ -175,6 +178,9 @@
 
 # The following background points represent the baseline noise in the diffraction data.
 print(ed.section('Add background'))
+project.experiments["npd"].background_type = "point"
+project.experiments["npd"].show_supported_background_types()
+project.experiments["npd"].show_current_background_type()
 project.experiments["npd"].background.add(x=11.0, y=206.1624)
 project.experiments["npd"].background.add(x=15.0, y=194.75)
 project.experiments["npd"].background.add(x=20.0, y=194.505)
@@ -185,14 +191,13 @@
 project.experiments["npd"].background.add(x=153.0, y=226.0595)
 project.experiments["npd"].background.show()
 
-project.experiments["xrd"].background.add(x=11.0, y=141.8516)
-project.experiments["xrd"].background.add(x=13.0, y=102.8838)
-project.experiments["xrd"].background.add(x=16.0, y=78.0551)
-project.experiments["xrd"].background.add(x=20.0, y=124.0121)
-project.experiments["xrd"].background.add(x=30.0, y=123.7123)
-project.experiments["xrd"].background.add(x=50.0, y=120.8266)
-project.experiments["xrd"].background.add(x=90.0, y=113.7473)
-project.experiments["xrd"].background.add(x=110.0, y=132.4643)
+project.experiments["xrd"].background_type = "chebyshev polynomial"
+project.experiments["xrd"].background.add(order=0, coef=119.195)
+project.experiments["xrd"].background.add(order=1, coef=6.221)
+project.experiments["xrd"].background.add(order=2, coef=-45.725)
+project.experiments["xrd"].background.add(order=3, coef=8.119)
+project.experiments["xrd"].background.add(order=4, coef=54.552)
+project.experiments["xrd"].background.add(order=5, coef=-20.661)
 project.experiments["xrd"].background.show()
 
 print(ed.section('Show experiments as CIF. Now the background points are included'))
@@ -221,10 +226,10 @@
 
 project.analysis.show_free_params()
 
-print(ed.section('Set refinement strategy'))
-project.analysis.show_available_refinement_strategies()
-project.analysis.show_current_refinement_strategy()
-#project.analysis.refinement_strategy = 'single'
+print(ed.section('Set fit mode'))
+project.analysis.show_available_fit_modes()
+project.analysis.show_current_fit_mode()
+#project.analysis.fit_mode = 'single'
 
 print(ed.section('Set fitting engine'))
 project.analysis.show_available_minimizers()
@@ -250,7 +255,7 @@
 project.analysis.show_meas_vs_calc_chart(expt_id="xrd", x_min=26, x_max=28, show_residual=True)
 
 print(ed.section('Change calculator'))
-project.analysis.show_available_calculators()
+project.analysis.show_supported_calculators()
 project.analysis.current_calculator = 'cryspy'
 
 print(ed.section('Start 3rd fitting'))
@@ -260,13 +265,13 @@
 project.analysis.show_meas_vs_calc_chart(expt_id="npd", x_min=62, x_max=66, show_residual=True)
 project.analysis.show_meas_vs_calc_chart(expt_id="xrd", x_min=26, x_max=28, show_residual=True)
 
-print(ed.section('Change refinement strategy'))
-project.analysis.show_available_refinement_strategies()
-project.analysis.show_current_refinement_strategy()
-project.analysis.refinement_strategy = 'combined'
+print(ed.section('Change fit mode'))
+project.analysis.show_available_fit_modes()
+project.analysis.show_current_fit_mode()
+project.analysis.fit_mode = 'joint'
 
 print(ed.section('Change calculator'))
-project.analysis.show_available_calculators()
+project.analysis.show_supported_calculators()
 project.analysis.show_current_calculator()
 project.analysis.current_calculator = 'crysfml'
 
@@ -277,6 +282,9 @@
 project.analysis.show_meas_vs_calc_chart(expt_id="npd", x_min=62, x_max=66, show_residual=True)
 project.analysis.show_meas_vs_calc_chart(expt_id="xrd", x_min=26, x_max=28, show_residual=True)
 
+# Show analysis as CIF
+project.analysis.show_as_cif()
+
 # Save the project state after analysis
 project.save()
 

src/easydiffraction/__init__.py

@@ -11,10 +11,8 @@
 )
 
 # Experiment creation and collection management
-from easydiffraction.experiments.experiments import (
-    Experiment,
-    Experiments
-)
+from easydiffraction.experiments.experiment import Experiment
+from easydiffraction.experiments.experiments import Experiments
 
 # Analysis
 from easydiffraction.analysis.analysis import Analysis