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Do not fit escape peaks #16

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Merged
pblowey merged 1 commit into from
Mar 4, 2026
Merged

Do not fit escape peaks #16

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6 changes: 4 additions & 2 deletions src/pymca_zocalo/internals.py
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Original file line number Diff line number Diff line change
Expand Up @@ -223,7 +223,7 @@ def spectrum_to_mca(channel_counts, calib, output_file, input_file, selection):
f"#S 1 {input_file} {selection['entry']}",
f"#D {timestamp}",
"#@MCA %16C",
f"#@CHANN {len(channel_counts)} 0 {len(channel_counts)-1} 1",
f"#@CHANN {len(channel_counts)} 0 {len(channel_counts) - 1} 1",
f"#@CALIB {calib['zero']} {calib['gain']} 0.0",
]
header = "\n".join(header)
Expand Down Expand Up @@ -401,7 +401,9 @@ def run_auto_pymca(
)
if cutoff_channel < fit_xmax:
config_dict["fit"]["xmax"] = cutoff_channel
# Do not fit scattering or escape peaks - these are not of interest and can cause issues with fitting if present
config_dict["fit"]["scatterflag"] = 0
config_dict["fit"]["escapeflag"] = 0
config_dict.write(cfg_file)

if not cfg_file.exists():
Expand Down Expand Up @@ -475,7 +477,7 @@ def run_auto_pymca(
</table></td></tr>
<tr><td>Automated PyMca results<br /><pre>{pymca_output}</pre><a href="http://www.diamond.ac.uk/dms/MX/Common/Interpreting-AutoPyMCA/Interpreting%20AutoPyMCA.pdf">Guide to AutoPyMCA</a> (pdf)</td></tr>
<tr><td><img src="{plot_output_file}" /></td></tr>
<tr><td><img src="{snapshot_dir/snapshot_filename}" alt="Snapshot not taken" width=640 /></td></tr></table>
<tr><td><img src="{snapshot_dir / snapshot_filename}" alt="Snapshot not taken" width=640 /></td></tr></table>
"""

with open(html_file, "w") as f:
Expand Down
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