Add some documentation on the calibration process - #141
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Pull request overview
This PR expands the Sphinx documentation by adding a new calibration guide and introducing a set of API reference pages for many hexsample modules, along with a few documentation-path fixes to make included assets resolve correctly.
Changes:
- Added a new
Calibrationdocumentation page and linked it from the main docs index under a new “Technical info” section. - Added initial API reference
.rstpages (autodoc stubs and a few narrative pages) for multiplehexsample.*modules. - Updated some documentation asset paths (e.g.,
figure::/literalinclude::) to use correct relative locations.
Reviewed changes
Copilot reviewed 10 out of 25 changed files in this pull request and generated 5 comments.
Show a summary per file
| File | Description |
|---|---|
| docs/index.rst | Adds a “Technical info” toctree entry for the new calibration docs (also where module toctree wiring needs alignment with docs/api/). |
| docs/calibration.rst | New narrative documentation describing the calibration process (noise/pedestal + gain). |
| docs/api/analysis.rst | New API reference stub for hexsample.analysis. |
| docs/api/base.rst | New API page with narrative + autodoc for hexsample.base. |
| docs/api/calibration.rst | New API reference stub for hexsample.calibration. |
| docs/api/cli.rst | New API page for hexsample.cli (intro + autodoc). |
| docs/api/clustering.rst | New API reference stub for hexsample.clustering. |
| docs/api/digi.rst | Updates/introduces the hexsample.digi API page and fixes literalinclude path. |
| docs/api/display.rst | New API reference stub for hexsample.display. |
| docs/api/fileio.rst | Fixes literalinclude paths and includes autodoc for hexsample.fileio. |
| docs/api/hexagon.rst | Fixes the figure path for the hexagonal layouts image. |
| docs/api/legacy.rst | New API reference stub for hexsample.legacy. |
| docs/api/mc.rst | New API reference stub for hexsample.mc. |
| docs/api/pipeline.rst | New API page for hexsample.pipeline (narrative + autodoc). |
| docs/api/pretty.rst | New API page for hexsample.pretty (narrative + autodoc). |
| docs/api/readout.rst | New API reference stub for hexsample.readout. |
| docs/api/recon.rst | New API reference stub for hexsample.recon. |
| docs/api/resolution.rst | New API reference stub for hexsample.resolution. |
| docs/api/rng.rst | New API page for hexsample.rng (narrative + autodoc). |
| docs/api/roi.rst | New API page for hexsample.roi (narrative + autodoc). |
| docs/api/sensor.rst | New API reference stub for hexsample.sensor. |
| docs/api/shell.rst | New API reference stub for hexsample.shell. |
| docs/api/source.rst | New API page for hexsample.source (narrative, examples + autodoc). |
| docs/api/tasks.rst | New API page for hexsample.tasks (intro + autodoc). |
| docs/api/xpol.rst | New API reference stub for hexsample.xpol. |
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| Basic algorithm: take the pixel the highest value, remove it along with the 8 | ||
| pixels around (in a rectangular sense, which makes the things easier to | ||
| implement and reason about with numpy arrays). |
| we are clipping the negative part with the zero suppression. The algorithm | ||
| is accumulating the sum of the squares, which works out of the box. | ||
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| -> Issue for the new algorithm for pedestal and noise. |
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| This will produce a HDF5 file with two matrices, one with the noise values, | ||
| and one with the number of hits per pixels. | ||
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| If there are no hits for a specific pixel, we just use the average of the pixels | ||
| with hits. |
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| Two-pass processes. We need a monochromatic source, so that we know the | ||
| average number of electrons/holes produced. | ||
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| The process is based on a chisquare that can be minimized with respect to the | ||
| gain. The effect of the threshold introduces a bias, which can be corrected with |
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