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fix(lamni,flomni): create documentation folder before writing the tomo PDF report

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PDFWriter does not create directories, so tomo_scan() failed with
FileNotFoundError when ~/data/raw/documentation did not exist. Also add an omny
TODO for porting the remaining ~/Data10 paths and the same folder fix.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_016gUjUT2xCNpnBQkThn3CqP
This commit is contained in:
holler
2026-09-29 13:07:46 +02:00
committed by holler
co-authored by Claude Sonnet 5
parent 7753dfff38
commit 0d42cb303b
3 changed files with 48 additions and 0 deletions
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csaxs_bec/bec_ipython_client/plugins/LamNI/lamni.py
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@@ -2492,6 +2492,7 @@ class LamNI(TomoQueueMixin, LamNIAlignmentMixin, LamNIOpticsMixin, LamniGuiTools
user_target = os.path.expanduser(
f"~/data/raw/documentation/tomo_scan_ID_{self.tomo_id}.pdf"
)
os.makedirs(os.path.dirname(user_target), exist_ok=True)
with PDFWriter(user_target) as file:
self._add_psi_footer(file)
# PDFWriter (bec_lib) has no public image API -- reach into its
csaxs_bec/bec_ipython_client/plugins/flomni/flomni.py
+1
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@@ -4289,6 +4289,7 @@ class Flomni(
user_target = os.path.expanduser(
f"~/data/raw/documentation/tomo_scan_ID_{self.tomo_id}.pdf"
)
os.makedirs(os.path.dirname(user_target), exist_ok=True)
with PDFWriter(user_target) as file:
self._add_psi_footer(file)
# PDFWriter (bec_lib) has no public image API -- reach into its
csaxs_bec/bec_ipython_client/plugins/omny/AI_docs/TODO_data10_to_new_data_structure.md
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@@ -0,0 +1,46 @@
# TODO: OMNY still uses the old `~/Data10` layout, and its PDF report can fail on a missing folder
LamNI and flomni write their files under the new data structure (`~/data/raw/...`).
OMNY still points at the old `~/Data10/...` tree in several places and needs porting.
Not done yet, to avoid conflicting with other in-progress OMNY changes.
## 1. Port `~/Data10` paths to the new data structure
Where OMNY (`csaxs_bec/bec_ipython_client/plugins/omny/`) still uses `~/Data10`:
| File | Line | Path | LamNI/flomni equivalent |
|---|---|---|---|
| `omny.py` | 1217 | `tomo_reconstruct(base_path="~/Data10/specES1")` | `~/data/raw/logs/reconstruction_queue` |
| `omny.py` | 1236 | `~/Data10/specES1/dat-files/tomography_scannumbers.txt` | `~/data/raw/logs/tomography_scannumbers.txt` |
| `omny.py` | 1484 | `~/Data10/documentation/tomo_scan_ID_<id>.pdf` | `~/data/raw/documentation/tomo_scan_ID_<id>.pdf` |
| `omny.py` | 1489 | `xterm /work/sls/spec/local/XOMNY/bin/upload/upload_last_pon.sh &` | old spec upload script, check it still applies |
| `x_ray_eye_align.py` | 392 | `~/Data10/specES1/internal/xrayeye_alignmentvalues` | `~/data/raw/logs/xrayeye_alignmentvalues/` (timestamped HDF5) |
| `omny_alignment_mixin.py` | 62 | `~/Data10/specES1/internal/` | see the same alignment-values location |
The reconstruction queue folder in the new layout is created and written by the shared
`PtychoReconstructor.write()` (`OMNY_shared/omny_general_tools.py`), which OMNY does not use
yet. See also `TODO_tomo_reconstruct_stale_scan_list.md` (already ported to flomni and LamNI,
so switching OMNY to the shared reconstructor would cover both items).
## 2. Create the documentation folder if it does not exist
`OMNY.write_pdf_report()` (`omny.py:1439`) opens `PDFWriter(user_target)` without creating the
target folder first. `PDFWriter.close()` calls fpdf's `output(path)`
(`bec_lib/pdf_writer.py:90`), which does not create directories, so on an account without the
folder `tomo_scan()` fails with:
```
FileNotFoundError: [Errno 2] No such file or directory: '.../documentation/tomo_scan_ID_0.pdf'
```
Seen on LamNI; flomni had the identical pattern. Both are fixed by creating the folder before
the writer is opened:
```python
os.makedirs(os.path.dirname(user_target), exist_ok=True)
with PDFWriter(user_target) as file:
```
Apply the same line in `OMNY.write_pdf_report()`, and use the new-structure path from item 1.
Note the later steps in that method (the `upload_last_pon.sh` call and the logbook message)
only run if the PDF write succeeds.