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docs/CBOR.md: sync field names/types with the serializer

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Bring the protocol doc in line with CBORStream2Serializer/Deserializer:

- reflection dist_ewald -> rp (dist_ewald is the spot field, not the
  reflection field)
- az_int_std -> az_int_profile_std, az_int_count -> az_int_profile_count
- threshold_energy typed as Map(string -> float), not float
- end_date typed as string (it is serialized as a plain text string, with
  no datetime tag, unlike arm_date)
- add missing reflection fields: phi, zeta, image_scale_corr
- add missing spot fields: image, and indexed-only h, k, l, dist_ewald
- add image indexing_lattice_count and end indexed_lattice_count
- drop the duplicated image_scale_factor row in the End table

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
This commit is contained in:
leonarski_f
2026-06-16 19:11:37 +02:00
co-authored by Claude Opus 4.8
parent 6479b91e50
commit caff857d8a
1 changed files with 15 additions and 6 deletions
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docs/CBOR.md
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@@ -68,7 +68,7 @@ There are minor differences at the moment:
| max_extra_lattices | uint64 | Maximum number of extra lattices | |
| storage_cell_number | uint64 (optional) | Number of storage cells used by JUNGFRAU | |
| storage_cell_delay | Rational | Delay of storage cells in JUNGFRAU | |
| threshold_energy | float | Threshold energy for EIGER detector \[eV\] | |
| threshold_energy | Map(string -> float) | Per-channel threshold energy \[eV\] (map of channel name to value) | |
| image_dtype | string | Pixel bit type (e.g. uint16) | X |
| unit_cell | object (optional) | Unit cell of the system: a, b, c \[angstrom\] and alpha, beta, gamma \[degree\] | |
| az_int_q_bin_count | uint64 | Number of azimuthal integration bins in the radial direction | |
@@ -139,6 +139,11 @@ See [DECTRIS documentation](https://github.com/dectris/documentation/tree/main/s
| - ice_ring | bool | spot in resolution range for ice rings | | |
| - indexed | bool | indexed solution | | |
| - latt | int64 | Lattice to which the peak belongs (negative number = not indexed) | | |
| - image | int64 | image number the spot belongs to | | |
| - h | int64 | Miller index (indexed spots only) | | |
| - k | int64 | Miller index (indexed spots only) | | |
| - l | int64 | Miller index (indexed spots only) | | |
| - dist_ewald | float | distance to Ewald sphere \[Angstrom^-1\] (indexed spots only) | | |
| reflections | Array(object) | Reflections: | | |
| - h | int64 | Miller index | | |
| - k | int64 | Miller index | | |
@@ -152,18 +157,22 @@ See [DECTRIS documentation](https://github.com/dectris/documentation/tree/main/s
| - bkg | float | mean background value (photons) | | |
| - sigma | float | standard deviation, estimated from counting statistics (photons) | | |
| - image | float | image number (present for each spot) | | |
| - dist_ewald | float | distance to Ewald sphere (present only for indexed spots) | | |
| - rp | float | Distance to Ewald sphere \[Angstrom^-1\] | | |
| - rlp | float | Reciprocal Lorentz and polarization corrections | | |
| - partiality | float | Partiality of the reflection | | |
| - phi | float | phi angle from XDS: difference from middle of current frame, not absolute \[deg\] | | |
| - zeta | float | Lorentz zeta factor (reciprocal-space geometry term) | | |
| - image_scale_corr | float | Per-image scale correction; I_true = image_scale_corr * I | | |
| spot_count | uint64 | Spot count | | |
| spot_count_ice_rings | uint64 | Number of spots within identified rings (experimental) | | |
| spot_count_low_res | uint64 | Number of spots in low resolution (prior to filtering) | | |
| spot_count_indexed | uint64 | Number of spots which fit indexing solution within a given tolerance | | |
| az_int_profile | Array(float) | Azimuthal integration results, use az_int_bin_to_q from start message for legend | | |
| | | NaN is used for empty bins and has to be taken care by the receiver | | |
| az_int_std | Array(float) | Standard deviation for azimuthal integration. (NaN for less than 2 samples) | | |
| az_int_count | Array(uint64) | Number of pixels contributing to azimuthal bin | | |
| az_int_profile_std | Array(float) | Standard deviation for azimuthal integration. (NaN for less than 2 samples) | | |
| az_int_profile_count | Array(uint64) | Number of pixels contributing to azimuthal bin | | |
| indexing_result | bool | Indexing successful | | |
| indexing_lattice_count | int64 | Number of indexing lattices found for this image | | |
| indexing_lattice | Array(9 * float) | Indexing result real lattice; present only if indexed | | X |
| indexing_extra_lattices | Array(Array(9*float)) | Additional indexed lattices (orientation variants); present only if found | | |
| indexing_unit_cell | object | Indexing result unit cell: a, b, c \[angstrom\] and alpha, beta, gamma \[degree\]; present only if indexed | | X |
@@ -271,7 +280,7 @@ See [DECTRIS documentation](https://github.com/dectris/documentation/tree/main/s
| magic_number | uint64 | Number used to describe version of the Jungfraujoch data interface - to allow to detect inconsistency between sender and receiver | |
| series_unique_id | string | Unique text ID of the series (run_name parameter) | X |
| series_id | uint64 | Unique numeric ID of the series (run_number parameter) | X |
| end_date | date | Approximate end date | |
| end_date | string | Approximate end date | |
| max_image_number | uint64 | Number of image with the highest number; counted from 1 to distinguish zero images and one image | |
| images_collected | uint64 | Number of images collected | |
| images_sent_to_write | uint64 | Number of images sent to writer; if writer queues were full, it is possible this is less than images collected | |
@@ -306,9 +315,9 @@ See [DECTRIS documentation](https://github.com/dectris/documentation/tree/main/s
| error_pixel_count | Array(int32) | Per-image error pixel count | |
| image_scale_factor | Array(float) | Per-image scale factor, if scaling/merging was performed | |
| integrated_reflections | Array(int32) | Per-image count of integrated reflections | |
| indexed_lattice_count | Array(int32) | Per-image count of indexed lattices | |
| niggli_class | Array(uint8) | Per-image Niggli class identifier for indexed images; 0 if unavailable | |
| pixel_sum | Array(int64) | Per-image sum of all valid pixels, excluding error/saturated pixels | |
| image_scale_factor | Array(float) | Scaling result: Image scale factor (g) | |
| image_scale_mosaicity | Array(float) | Scaling result: Image scale mosaicity \[deg\] | |
| image_scale_b_factor | Array(float) | Scaling result: Image scale B factor \[Angstrom^2\] | |
| image_scale_cc | Array(float) | Scaling result: Image scale CC | |