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Merged
rozyczko merged 34 commits into from
Apr 4, 2025
Merged

New params support + fixes for the new EDA #171

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2fc48b1
initial conversion to the new parameter syntax
rozyczko Jan 14, 2025
697436f
added new Descriptors and fixed ruff
rozyczko Jan 14, 2025
4c787af
use ruff 0.9, since 0.8.x didn't give good enough info
rozyczko Jan 14, 2025
68df4b5
rely on `new_param` branch of EXC
rozyczko Jan 14, 2025
56b5ee2
assure exp names are correct
rozyczko Jan 30, 2025
1af34a5
ruff
rozyczko Jan 30, 2025
d5cd717
minor fixes
rozyczko Feb 2, 2025
512bfcf
ruff
rozyczko Feb 3, 2025
c459983
assign interface when necessary
rozyczko Feb 4, 2025
59a7ddf
_pd_calib.2theta_offset in parameters for display
rozyczko Feb 7, 2025
1fe8c4e
minor changes for multiphase
rozyczko Feb 10, 2025
107675c
added optional to some phase params to make possible editing CIF in
rozyczko Feb 12, 2025
48c2a9c
fix offset setup
rozyczko Feb 12, 2025
af4b833
added error parser for integers
rozyczko Feb 13, 2025
ca28ab7
fixed reading of errors in phase cif
rozyczko Feb 14, 2025
c7a7b53
tof stuff from new_param_tof
rozyczko Feb 14, 2025
7a9b9fd
changes after merging DescriptorAny in EasyCrystallography
rozyczko Feb 14, 2025
fd6679e
fixed typo
rozyczko Feb 15, 2025
1cb2aa8
added updated version of dataBlockToCif
rozyczko Feb 17, 2025
e7e82fb
ruff fixes.
rozyczko Feb 17, 2025
68d4300
Fixed TOF profile calcs. Fixed typos
rozyczko Feb 18, 2025
bff8037
minor fixes and performance impromevents
rozyczko Feb 19, 2025
f543b62
ruff
rozyczko Feb 19, 2025
ce4cb41
Merge branch 'develop' into new_param
rozyczko Feb 21, 2025
37de5e7
fix for multiphase scale issue not being properly set up after fitting
rozyczko Feb 21, 2025
a4bcfe7
ruff. what else?
rozyczko Feb 21, 2025
1eafc1e
add fix for exp names, not just tof.
rozyczko Feb 22, 2025
810fc88
Added bridge link for intermediate updates
rozyczko Feb 26, 2025
760db4e
fixed phase update for multiphase cases
rozyczko Mar 4, 2025
d3e258d
minor fix for ToF
rozyczko Mar 13, 2025
c22b4bf
fixes for experiment update
rozyczko Mar 19, 2025
67406dc
be careful with the offset
rozyczko Mar 20, 2025
d5bd9bc
all deps are now released.
rozyczko Mar 24, 2025
0b5dd3f
offset correction is necessary
rozyczko Mar 26, 2025
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2 changes: 1 addition & 1 deletion examples_old/PDF/Fitting_PDF_Profile_Ni.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -301,7 +301,7 @@
"print(f\"The goodness of fit (chi2) is: {result.reduced_chi}\")\n",
"print(\"The optimized parameters are:\")\n",
"for param in job.get_fit_parameters():\n",
" print(f\"{param.name}: {param.raw_value} +\\- {param.error} {param.unit}\") "
" print(f\"{param.name}: {param.value} +\\- {param.variance} {param.unit}\") "
]
},
{
Expand Down
80 changes: 40 additions & 40 deletions examples_old/PDF/Fitting_PDF_Profile_Si.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -481,12 +481,12 @@
"outputs": [],
"source": [
"# Add initial data used in EasyDiffraction to pandas DataFrame\n",
"df_case1['ezd_ini'] = [phases_Si1[0].scale.raw_value, \n",
" parameters1.delta2.raw_value, \n",
" phase1_patterns1.cell.length_a.raw_value, \n",
" phase1_patterns1.atoms[0].adp.Uiso.raw_value, \n",
" parameters1.qdamp.raw_value, \n",
" parameters1.qbroad.raw_value]"
"df_case1['ezd_ini'] = [phases_Si1[0].scale.value, \n",
" parameters1.delta2.value, \n",
" phase1_patterns1.cell.length_a.value, \n",
" phase1_patterns1.atoms[0].adp.Uiso.value, \n",
" parameters1.qdamp.value, \n",
" parameters1.qbroad.value]"
]
},
{
Expand Down Expand Up @@ -584,7 +584,7 @@
"df_case1['ezd_fit'] = pd.Series(dtype='float64')\n",
"\n",
"for i in range(len(job_Si1.get_fit_parameters())):\n",
" df_case1['ezd_fit'][job_Si1.get_fit_parameters()[i].name] = job_Si1.get_fit_parameters()[i].raw_value\n",
" df_case1['ezd_fit'][job_Si1.get_fit_parameters()[i].name] = job_Si1.get_fit_parameters()[i].value\n",
"df_case1"
]
},
Expand All @@ -611,7 +611,7 @@
"print(\"The optimized parameters are:\")\n",
"\n",
"for param in job_Si1.get_fit_parameters():\n",
" print(f\"{param.name}: {param.raw_value} +\\- {param.error} {param.unit}\") "
" print(f\"{param.name}: {param.value} +\\- {param.variance} {param.unit}\") "
]
},
{
Expand Down Expand Up @@ -807,10 +807,10 @@
"outputs": [],
"source": [
"# Add initial data used in EasyDiffraction to pandas DataFrame\n",
"df_case2['ezd_ini'] = [phases_Si2[0].scale.raw_value, \n",
" parameters2.delta2.raw_value, \n",
" phase1_patterns2.cell.length_a.raw_value, \n",
" phase1_patterns2.atoms[0].adp.Uiso.raw_value]"
"df_case2['ezd_ini'] = [phases_Si2[0].scale.value, \n",
" parameters2.delta2.value, \n",
" phase1_patterns2.cell.length_a.value, \n",
" phase1_patterns2.atoms[0].adp.Uiso.value]"
]
},
{
Expand Down Expand Up @@ -873,10 +873,10 @@
"metadata": {},
"outputs": [],
"source": [
"df_case2['ezd_ini'] = [phases_Si2[0].scale.raw_value, \n",
" parameters2.delta2.raw_value, \n",
" phase1_patterns2.cell.length_a.raw_value, \n",
" phase1_patterns2.atoms[0].adp.Uiso.raw_value\n",
"df_case2['ezd_ini'] = [phases_Si2[0].scale.value, \n",
" parameters2.delta2.value, \n",
" phase1_patterns2.cell.length_a.value, \n",
" phase1_patterns2.atoms[0].adp.Uiso.value\n",
" ]\n",
"df_case2"
]
Expand Down Expand Up @@ -918,7 +918,7 @@
"df_case2['ezd_fit'] = pd.Series(dtype='float64')\n",
"\n",
"for i in range(len(job_Si2.get_fit_parameters())):\n",
" df_case2['ezd_fit'][job_Si2.get_fit_parameters()[i].name] = job_Si2.get_fit_parameters()[i].raw_value\n",
" df_case2['ezd_fit'][job_Si2.get_fit_parameters()[i].name] = job_Si2.get_fit_parameters()[i].value\n",
"df_case2"
]
},
Expand All @@ -944,7 +944,7 @@
"print(f\"The goodness of fit (chi2) is: {result_Si2.reduced_chi}\")\n",
"print(\"The optimized parameters are:\")\n",
"for param in job_Si2.get_fit_parameters():\n",
" print(f\"{param.name}: {param.raw_value} +\\- {param.error} {param.unit}\") "
" print(f\"{param.name}: {param.value} +\\- {param.variance} {param.unit}\") "
]
},
{
Expand Down Expand Up @@ -1139,12 +1139,12 @@
"outputs": [],
"source": [
"# Add initial data used in EasyDiffraction to pandas DataFrame\n",
"df_case3['ezd_ini'] = [phases_Si3[0].scale.raw_value, \n",
" parameters3.delta2.raw_value, \n",
" phase1_patterns3.cell.length_a.raw_value, \n",
" phase1_patterns3.atoms[0].adp.Uiso.raw_value, \n",
" parameters3.qdamp.raw_value, \n",
" parameters3.qbroad.raw_value]"
"df_case3['ezd_ini'] = [phases_Si3[0].scale.value, \n",
" parameters3.delta2.value, \n",
" phase1_patterns3.cell.length_a.value, \n",
" phase1_patterns3.atoms[0].adp.Uiso.value, \n",
" parameters3.qdamp.value, \n",
" parameters3.qbroad.value]"
]
},
{
Expand Down Expand Up @@ -1236,7 +1236,7 @@
"df_case3['ezd_fit'] = pd.Series(dtype='float64')\n",
"\n",
"for i in range(len(job_Si3.get_fit_parameters())):\n",
" df_case3['ezd_fit'][job_Si3.get_fit_parameters()[i].name] = job_Si3.get_fit_parameters()[i].raw_value\n",
" df_case3['ezd_fit'][job_Si3.get_fit_parameters()[i].name] = job_Si3.get_fit_parameters()[i].value\n",
"df_case3"
]
},
Expand All @@ -1261,7 +1261,7 @@
"print(\"The optimized parameters are:\")\n",
"\n",
"for param in job_Si3.get_fit_parameters():\n",
" print(f\"{param.name}: {param.raw_value} +\\- {param.error} {param.unit}\") "
" print(f\"{param.name}: {param.value} +\\- {param.variance} {param.unit}\") "
]
},
{
Expand Down Expand Up @@ -1441,12 +1441,12 @@
"outputs": [],
"source": [
"# Add initial data used in EasyDiffraction to pandas DataFrame\n",
"df_case4['ezd_ini'] = [phases_Si4[0].scale.raw_value, \n",
" parameters4.delta2.raw_value, \n",
" phase1_patterns4.cell.length_a.raw_value, \n",
" phase1_patterns4.atoms[0].adp.Uiso.raw_value, \n",
" parameters4.qdamp.raw_value, \n",
" parameters4.qbroad.raw_value]"
"df_case4['ezd_ini'] = [phases_Si4[0].scale.value, \n",
" parameters4.delta2.value, \n",
" phase1_patterns4.cell.length_a.value, \n",
" phase1_patterns4.atoms[0].adp.Uiso.value, \n",
" parameters4.qdamp.value, \n",
" parameters4.qbroad.value]"
]
},
{
Expand Down Expand Up @@ -1541,7 +1541,7 @@
"df_case4['ezd_fit'] = pd.Series(dtype='float64')\n",
"\n",
"for i in range(len(job_Si4.get_fit_parameters())):\n",
" df_case4['ezd_fit'][job_Si4.get_fit_parameters()[i].name] = job_Si4.get_fit_parameters()[i].raw_value\n",
" df_case4['ezd_fit'][job_Si4.get_fit_parameters()[i].name] = job_Si4.get_fit_parameters()[i].value\n",
"df_case4"
]
},
Expand All @@ -1566,7 +1566,7 @@
"print(\"The optimized parameters are:\")\n",
"\n",
"for param in job_Si4.get_fit_parameters():\n",
" print(f\"{param.name}: {param.raw_value} +\\- {param.error} {param.unit}\") "
" print(f\"{param.name}: {param.value} +\\- {param.variance} {param.unit}\") "
]
},
{
Expand Down Expand Up @@ -1735,10 +1735,10 @@
"outputs": [],
"source": [
"# Add initial data used in EasyDiffraction to pandas DataFrame\n",
"df_case5['ezd_ini'] = [phases_Si5[0].scale.raw_value, \n",
" parameters5.delta2.raw_value, \n",
" phase1_patterns5.cell.length_a.raw_value, \n",
" phase1_patterns5.atoms[0].adp.Uiso.raw_value]"
"df_case5['ezd_ini'] = [phases_Si5[0].scale.value, \n",
" parameters5.delta2.value, \n",
" phase1_patterns5.cell.length_a.value, \n",
" phase1_patterns5.atoms[0].adp.Uiso.value]"
]
},
{
Expand Down Expand Up @@ -1828,7 +1828,7 @@
"df_case5['ezd_fit'] = pd.Series(dtype='float64')\n",
"\n",
"for i in range(len(job_Si5.get_fit_parameters())):\n",
" df_case5['ezd_fit'][job_Si5.get_fit_parameters()[i].name] = job_Si5.get_fit_parameters()[i].raw_value\n",
" df_case5['ezd_fit'][job_Si5.get_fit_parameters()[i].name] = job_Si5.get_fit_parameters()[i].value\n",
"df_case5"
]
},
Expand All @@ -1853,7 +1853,7 @@
"print(\"The optimized parameters are:\")\n",
"\n",
"for param in job_Si5.get_fit_parameters():\n",
" print(f\"{param.name}: {param.raw_value} +\\- {param.error} {param.unit}\") "
" print(f\"{param.name}: {param.value} +\\- {param.variance} {param.unit}\") "
]
},
{
Expand Down
2 changes: 1 addition & 1 deletion examples_old/PDF2/Fitting_PDF_Profile.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -301,7 +301,7 @@
"print(f\"The goodness of fit (chi2) is: {result.reduced_chi}\")\n",
"print(\"The optimized parameters are:\")\n",
"for param in job.get_fit_parameters():\n",
" print(f\"{param.name}: {param.raw_value} +\\- {param.error} {param.unit}\") "
" print(f\"{param.name}: {param.value} +\\- {param.variance} {param.unit}\") "
]
},
{
Expand Down
2 changes: 1 addition & 1 deletion examples_old/PDF2/Ni_fitting.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -66,7 +66,7 @@

print("The optimized parameters are:")
for param in fit_parameters:
print("{}: {}".format(param.name, param.raw_value))
print("{}: {}".format(param.name, param.value))

y_data = calculator.fit_func(x_data)

Expand Down
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