Skip to content

Improve reporting and plotting, switch default minimizer to LMFIT, and refresh tutorials #154

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
AndrewSazonov merged 17 commits into from
Apr 14, 2026
Merged

Improve reporting and plotting, switch default minimizer to LMFIT, and refresh tutorials #154

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
17 commits
Select commit Hold shift + click to select a range
b037ca1
Pass calculator to peak profile type filtering
AndrewSazonov Apr 13, 2026
7d40441
Filter background and extinction types by active calculator
AndrewSazonov Apr 13, 2026
a291d98
Format parameter value logging to display eight decimal places
AndrewSazonov Apr 13, 2026
fcc79ac
Restrict range validator for parameter values to 0.0 - 10.0
AndrewSazonov Apr 13, 2026
6e375a1
Improve logging for fitted parameters notes and warnings
AndrewSazonov Apr 13, 2026
9f0ce4b
Clean up
AndrewSazonov Apr 13, 2026
5d3ca0a
Update notebooks
AndrewSazonov Apr 13, 2026
6e9dc16
Add plotting of parameter correlations and measurement vs calculation…
AndrewSazonov Apr 13, 2026
417c956
Enhance summary reporting by adding uncertainty values for parameters…
AndrewSazonov Apr 13, 2026
0820e60
Change default minimizer type from BUMPS_LM to LMFIT_LEASTSQ
AndrewSazonov Apr 13, 2026
a502561
Update notebooks
AndrewSazonov Apr 13, 2026
e7b2dce
Update data index sha
AndrewSazonov Apr 13, 2026
89e9131
Fix return type
AndrewSazonov Apr 13, 2026
0355c52
Update tests
AndrewSazonov Apr 13, 2026
d153bcf
Bump dependencies
AndrewSazonov Apr 13, 2026
8a598bd
Move external data from easyscience/data/diffraction to diffraction/data
AndrewSazonov Apr 14, 2026
ec8db03
Update chi-square assertion in test_analyze_reduced_data
AndrewSazonov Apr 14, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
12,638 changes: 0 additions & 12,638 deletions docs/docs/tutorials/data/MAT005500.BS.bin02Double_0_int_c.histogramIgor
View file
Open in desktop

This file was deleted.

9,813 changes: 0 additions & 9,813 deletions docs/docs/tutorials/data/MAT005500.SE.bin02Double_0_int_c.histogramIgor
View file
Open in desktop

This file was deleted.

1 change: 0 additions & 1 deletion docs/docs/tutorials/data/lbco_project/summary.cif
View file
Open in desktop

This file was deleted.

2 changes: 1 addition & 1 deletion docs/docs/tutorials/ed-10.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -208,7 +208,7 @@
"source": [
"project.analysis.fit()\n",
"project.analysis.display.fit_results()\n",
"project.plotter.plot_param_correlations()"
"project.plotter.plot_param_correlations(threshold=0.75)"
]
},
{
Expand Down
2 changes: 1 addition & 1 deletion docs/docs/tutorials/ed-10.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -83,7 +83,7 @@
# %%
project.analysis.fit()
project.analysis.display.fit_results()
project.plotter.plot_param_correlations()
project.plotter.plot_param_correlations(threshold=0.75)

# %% [markdown]
# ## Plot Measured vs Calculated
Expand Down
5 changes: 2 additions & 3 deletions docs/docs/tutorials/ed-11.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -82,9 +82,8 @@
"metadata": {},
"outputs": [],
"source": [
"# Keep the auto-selected engine. Alternatively, you can uncomment the\n",
"# line below to explicitly set the engine to the required one.\n",
"# project.plotter.engine = 'plotly'"
"project.plotter.show_supported_engines()\n",
"project.plotter.show_current_engine()"
]
},
{
Expand Down
5 changes: 2 additions & 3 deletions docs/docs/tutorials/ed-11.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -21,9 +21,8 @@
# ## Set Plotting Engine

# %%
# Keep the auto-selected engine. Alternatively, you can uncomment the
# line below to explicitly set the engine to the required one.
# project.plotter.engine = 'plotly'
project.plotter.show_supported_engines()
project.plotter.show_current_engine()

# %%
# Set global plot range for plots
Expand Down
2 changes: 1 addition & 1 deletion docs/docs/tutorials/ed-13.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2646,7 +2646,7 @@
],
"metadata": {
"jupytext": {
"cell_metadata_filter": "tags,title,-all",
"cell_metadata_filter": "title,tags,-all",
"main_language": "python",
"notebook_metadata_filter": "-all"
}
Expand Down
2 changes: 2 additions & 0 deletions docs/docs/tutorials/ed-15.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -229,6 +229,8 @@
"metadata": {},
"outputs": [],
"source": [
"project.analysis.show_available_minimizers()\n",
"project.analysis.show_current_minimizer()\n",
"project.analysis.current_minimizer = 'lmfit'"
]
},
Expand Down
2 changes: 2 additions & 0 deletions docs/docs/tutorials/ed-15.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -74,6 +74,8 @@
experiment.extinction.radius.free = True

# %%
project.analysis.show_available_minimizers()
project.analysis.show_current_minimizer()
project.analysis.current_minimizer = 'lmfit'

# %%
Expand Down
48 changes: 15 additions & 33 deletions docs/docs/tutorials/ed-16.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -444,32 +444,14 @@
"cell_type": "markdown",
"id": "40",
"metadata": {},
"source": [
"#### Set Minimizer"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "41",
"metadata": {},
"outputs": [],
"source": [
"project.analysis.current_minimizer = 'lmfit'"
]
},
{
"cell_type": "markdown",
"id": "42",
"metadata": {},
"source": [
"#### Plot Measured vs Calculated (Before Fit)"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "43",
"id": "41",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -479,7 +461,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "44",
"id": "42",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -488,7 +470,7 @@
},
{
"cell_type": "markdown",
"id": "45",
"id": "43",
"metadata": {},
"source": [
"#### Set Fitting Parameters\n",
Expand All @@ -500,7 +482,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "46",
"id": "44",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -510,7 +492,7 @@
},
{
"cell_type": "markdown",
"id": "47",
"id": "45",
"metadata": {},
"source": [
"Bragg experiment parameters."
Expand All @@ -519,7 +501,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "48",
"id": "46",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -534,7 +516,7 @@
},
{
"cell_type": "markdown",
"id": "49",
"id": "47",
"metadata": {},
"source": [
"PDF experiment parameters."
Expand All @@ -543,7 +525,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "50",
"id": "48",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -556,7 +538,7 @@
},
{
"cell_type": "markdown",
"id": "51",
"id": "49",
"metadata": {},
"source": [
"#### Show Free Parameters"
Expand All @@ -565,7 +547,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "52",
"id": "50",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -574,7 +556,7 @@
},
{
"cell_type": "markdown",
"id": "53",
"id": "51",
"metadata": {},
"source": [
"#### Run Fitting"
Expand All @@ -583,7 +565,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "54",
"id": "52",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -594,7 +576,7 @@
},
{
"cell_type": "markdown",
"id": "55",
"id": "53",
"metadata": {},
"source": [
"#### Plot Measured vs Calculated (After Fit)"
Expand All @@ -603,7 +585,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "56",
"id": "54",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -613,7 +595,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "57",
"id": "55",
"metadata": {},
"outputs": [],
"source": [
Expand Down
6 changes: 0 additions & 6 deletions docs/docs/tutorials/ed-16.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -186,12 +186,6 @@
project.analysis.joint_fit_experiments.create(id='sepd', weight=0.7)
project.analysis.joint_fit_experiments.create(id='nomad', weight=0.3)

# %% [markdown]
# #### Set Minimizer

# %%
project.analysis.current_minimizer = 'lmfit'

# %% [markdown]
# #### Plot Measured vs Calculated (Before Fit)

Expand Down
Loading
Loading