Adds WIP changes and plot redesigns.

.claude/settings.local.json

@@ -78,7 +78,28 @@
       "Bash(python 21_2026_07_08_flex_j_mb.py)",
       "Bash(cd \"scripts/specimens\")",
       "Bash(python scripts/plots/01_composite.py)",
-      "Bash(git -c safe.directory='*' status --short -- source/2026_07_06 source/2026_07_08 scripts/specimens/18_2026_07_06_tensile_j.py scripts/specimens/19_2026_07_06_flex_j.py scripts/specimens/20_2026_07_08_tensile_j_mb.py scripts/specimens/21_2026_07_08_flex_j_mb.py data/D638 data/D790 README.md CLAUDE.md scripts/plots/01_composite.py assets/D638_composite.png assets/D790_composite.png)"
+      "Bash(git -c safe.directory='*' status --short -- source/2026_07_06 source/2026_07_08 scripts/specimens/18_2026_07_06_tensile_j.py scripts/specimens/19_2026_07_06_flex_j.py scripts/specimens/20_2026_07_08_tensile_j_mb.py scripts/specimens/21_2026_07_08_flex_j_mb.py data/D638 data/D790 README.md CLAUDE.md scripts/plots/01_composite.py assets/D638_composite.png assets/D790_composite.png)",
+      "Bash(uniq -c -w2)",
+      "Bash(git reset *)",
+      "Bash(git checkout *)",
+      "Bash(awk '{print $1}')",
+      "Bash(awk '{$1=\"\"; print}')",
+      "Bash(uv run *)",
+      "Bash(python3 -c \"import json,sys; r=json.load\\(sys.stdin\\); print\\('old job_id:', r['job_id'], 'print_profile_id:', r['print_profile_id']\\)\")",
+      "Bash(python3 -c \"import json; r=json.load\\(open\\('data/D790/H1.jsonl'\\)\\); print\\('new job_id:', r['job_id'], 'print_profile_id:', r['print_profile_id']\\)\")",
+      "Bash(git status *)",
+      "Bash(python3 -)",
+      "Bash(git add *)",
+      "Bash(git commit -m ' *)",
+      "Bash(uv run python3 -c ' *)",
+      "Bash(grep -o '\"print_date\": \"[^\"]*\"' ../Agentic-SLS-Database/data/jobs.jsonl 2>/dev/null | sort -u | tail -20 || echo \"no sibling repo found at that path\"; ls .. 2>/dev/null)",
+      "Bash(ln -s Inova-Mk1-Database ../Agentic-SLS-Database)",
+      "Bash(uv run python -c ' *)",
+      "Bash(xargs -I{} sh -c \"python3 -c \\\\\"import json;print\\(json.load\\(open\\('{}'\\)\\)['source_paths']\\)\\\\\"\")",
+      "Bash(echo \"exit: $?\")",
+      "Bash(pkill -f \"04_batch_details.py\")",
+      "Bash(ps -o etimes= -p 13716)",
+      "Bash(ps -o etimes=,pid=,cmd= -p 13716)"
     ]
   }
 }

CLAUDE.md

@@ -100,13 +100,16 @@ scripts/specimens/
   30_2026_07_23_flex_n.py               # Batch N flex — xlsx_only
   31_2026_07_23_tensile_nylon12white_fl.py  # FormLabs Nylon 12 White tensile control — xlsx_only
   32_2026_07_23_flex_nylon12white_fl.py     # FormLabs Nylon 12 White flex control — xlsx_only
+  33_2026_08_03_tensile_nylon11_batch1.py   # Batch O tensile, Nylon 11, Type IV (O10-O13) — xlsx_only
+  34_2026_08_03_tensile_nylon11_batch2.py   # Batch P tensile, Nylon 11, Type IV (P1-P6,P8-P12) — xlsx_only
+  35_2026_08_03_flex_nylon11_batch2.py      # Batch P flex, Nylon 11 (P1-P9) — xlsx_only
 
 data/
   D638/                                 # one JSONL per specimen (HF glob: data/D638/*.jsonl)
-    A1.jsonl ... N5.jsonl               # SLS specimens, named by sample_id
+    A1.jsonl ... P12.jsonl              # SLS specimens, named by sample_id
     PLA_TSR6.jsonl ... NYLON12_WHITE_FL_Sheet5.jsonl  # non-SLS controls (no sample_id)
   D790/
-    C1.jsonl ... N5.jsonl               # SLS specimens, named by sample_id
+    C1.jsonl ... P9.jsonl               # SLS specimens, named by sample_id
 ```
 
 ## File format notes — TestWorks 4.1 output
@@ -143,15 +146,19 @@ Same TestWorks framework, different schema. Notable renames you have to handle:
 
 ## Current state
 
-- `D638` config — 103 rows: 87 SLS across batches A-N (batch counts: A5 B5 C7 D5 E5 F5 G5 H3 I5 J4 J_MB5 K5 L6 M17 N5) + 3 PLA + 3 PETG + 5 FormLabs PA12GF + 5 FormLabs Nylon 12 White.
-- `D790` config — 81 rows: 71 SLS across batches C-N (batch counts: C9 D8 E10 F9 G4 H5 I5 J2 J_MB2 K3 L4 M5 N5) + 5 FormLabs PA12GF + 5 FormLabs Nylon 12 White.
-- **Batches K-N have `db_print_date=None`** (print jobs not yet backfilled into Database) — SLS rows through J/J_MB have Database FKs (2026-07-12 backfill: E ← 2026-06-07 (same as D), F ← 2026-06-13, G ← 2026-06-09, H ← 2026-06-24, I ← 2026-06-25, J/J_MB ← 2026-06-27 (`D790 and D638 and other objects`)); K, L, M, N still need the same treatment once their print jobs land.
+- `D638` config — 118 rows: 102 SLS across batches A-P (batch counts: A5 B5 C7 D5 E5 F5 G5 H3 I5 J4 J_MB5 K5 L6 M17 N5 O4 P11) + 3 PLA + 3 PETG + 5 FormLabs PA12GF + 5 FormLabs Nylon 12 White.
+- `D790` config — 90 rows: 80 SLS across batches C-P (batch counts: C9 D8 E10 F9 G4 H5 I5 J2 J_MB2 K3 L4 M5 N5 P9) + 5 FormLabs PA12GF + 5 FormLabs Nylon 12 White.
+- **Batches K-P have `db_print_date=None`** (print jobs not yet backfilled into Database) — SLS rows through J/J_MB have Database FKs (2026-07-12 backfill: E ← 2026-06-07 (same as D), F ← 2026-06-13, G ← 2026-06-09, H ← 2026-06-24, I ← 2026-06-25, J/J_MB ← 2026-06-27 (`D790 and D638 and other objects`)); K, L, M, N, O, P still need the same treatment once their print jobs land.
 - **`_lib.py` disambiguates same-date jobs by STL content.** Two 2026-06-27 prints share a date in Database; `resolve_database_fk` picks the one whose object list contains the standard's STL needle (`d638` / `d790`). Same fix will apply to any future same-date collision (e.g. 06-29 already has two jobs, though no ASTM specimens map there yet).
-- Total: 184 specimens, produced by 32 per-session scripts (some date folders — 2026_06_10, 2026_06_30, 2026_07_21 — contain more than one Test project/batch/specimen type).
+- Total: 208 specimens, produced by 35 per-session scripts (some date folders — 2026_06_10, 2026_06_30, 2026_07_21 — contain more than one Test project/batch/specimen type).
 - Batch I flex is missing TSR4 (excluded: `test_end_reason` is "Test Stopped", not a detected break) — sample_ids I1-I5 map to TSR{1,2,3,5,6}.
 - Batch H's 5 flex rows are `xlsx_only` (no raw TestRuns folder survived — see architectural decisions above); Batches K, L, M, N are `xlsx_only` too (no TestRuns/h5 handed off for those sessions at all, not just one project overwriting another) — every other row has full h5-derived curves.
 - **Batch J / J_MB (2026-07-06 print, tested 07/06 and 07/08) is the first split-batch label.** Both are the same physical print batch; `J` specimens were tested as-printed, `J_MB` specimens were media blasted post-print before testing. This deviates from the single-letter `batch_label` convention (see architectural decisions above) — deliberately, per user instruction, to keep the surface-treatment distinction visible without adding a new schema field. If more media-blast-vs-not comparisons get added, consider promoting this to a real `surface_treatment` field instead of continuing to overload `batch_label`.
 - **Batch M tensile (D638) is the first batch mixing two ASTM specimen types.** 5 Type I dogbones (`tensile_m.xlsx`, sample_ids M1-M5) plus 12 Type IV narrow-section specimens from the same print (`tensile_m_t4.xlsx`, M6-M17, `astm.type = "Type IV"`) — see `26_2026_07_21_tensile_m.py` / `27_2026_07_21_tensile_m_type4.py`, which share `batch_label="M"` and continue sample numbering via `process_session`'s `seq_start`. Per user instruction the Type IV specimens get their own figure (`assets/D638_type_iv.png`) rather than sharing the cluster/batch-averages/detail figures with the rest of Batch M — `TYPE_LINESTYLES` in `scripts/plots/_lib.py` flags which ASTM types get this treatment, and `02_batch_averages.py`/`03_batch_clusters.py`/`04_batch_details.py` all exclude them accordingly (different gauge geometry, not comparable to Type I). Within that dedicated figure, each of the 12 specimens gets its own labeled curve (`render_type_iv` in `01_controls.py`) rather than one grouped legend entry — ordered by `specimen_index` (= xlsx sheet order = physical test order) and labeled per `TYPE_IV_LABELS = [1,2,3,4,5,6,8,9,10,11,13,14]`, a user-supplied numbering with intentional gaps at 7 and 12 (specimen numbers that exist in the lab's own record-keeping but aren't part of this xlsx export).
+- **Batches O and P (2026-08-03) are the first use of Nylon 11 SLS powder.** Two separate prints (`material_class` stays `"SLS"` — powder identity isn't a schema field, so it's flagged in each row's `notes` instead), both ASTM D638 Type IV only; Batch P also has D790 flex specimens. xlsx export only (no TestRuns/h5), same as Batches K-N. Two mechanism changes landed to support this session:
+  - **`read_xlsx_scalars`/`read_xlsx_curve` now resolve a sheet by its own name (`"Sheet{n}"`), not tab position** (`_resolve_sheet_name` in `_lib.py`) — `nylon11_batch1.xlsx`'s tabs are physically reordered (Sheet1, Sheet4, Sheet2, Sheet3), which broke the old position-based lookup. No-op for every prior session, whose tabs already happened to be in order.
+  - **`process_session`'s `test_runs` tuples can now take an optional 4th element: an explicit sample number**, overriding the usual auto-increment. Batch O's lab records number its 4 specimens 10-13 (not 1-4); Batch P's tensile skips lab number 7 entirely (its own xlsx sheet 7 is annotated "SAMPLE 8"), giving sample_ids P1-P6, P8-P12.
+  - Being Type IV, O/P are excluded from the cluster/batch-average figures same as Batch M's Type IV (`TYPE_LINESTYLES`), but — unlike Batch M's Type IV, which stays in `01_controls.py`'s combined `assets/D638_type_iv.png` — they get normal standalone per-batch figures from `04_batch_details.py` (`assets/batches/D638_O.png`, `D638_P.png`, `D790_P.png`), since they're not a geometry variant of an existing batch's Type I specimens the way Batch M's is. New `TYPE_IV_DEDICATED_BATCHES = {"M"}` in `scripts/plots/_lib.py` scopes the old blanket Type IV exclusion in `04`'s `group_key` (and `01_controls.py`'s `is_type_variant`) to just Batch M, letting any other Type IV batch fall through to the normal per-batch treatment.
 - **`NYLON12_WHITE_FL` is a new `material_class`** (FormLabs Nylon 12 White SLS control, tested 2026-07-23, no `batch_label`/`sample_id`, no Database FK) — a second FormLabs reference material alongside `PA12GF_FL`, unfilled/white nylon rather than glass-filled. Per user instruction it's excluded from the cluster/batch-averages figures and rendered on its own (`{standard}_nylon12white_control.png`, see `scripts/plots/_lib.py`'s `NYLON_CONTROLS`). **D638 (tensile) `tensile_nylon12white_fl.xlsx` is a raw load/extension export with no gauge-length scalar in the file** — unlike D790 there's no chord-formula fallback for tensile, so strain/stress can't be derived from geometry alone. User confirmed the test used a 25mm-starting-length extensometer, so `31_2026_07_23_tensile_nylon12white_fl.py` sets `gauge_length_mm: 25` explicitly and `build_row_from_xlsx` derives strain = extension/gauge_length, stress = load/area from that (see the `gauge_length_mm` session key, added for this case — `geometry.gauge_length_mm` on xlsx_only rows is null unless a session declares it). D790 (flex) rows derive normally since flexural strain/stress only need width/thickness. **The D638 curves are cut at their stress peak for plotting only** (`VERTICAL_BREAK_MATERIALS` in `scripts/plots/_lib.py`) — past peak, the raw trace continues as extension keeps increasing after the specimen separates while load reads ~0, and with few points sampled through the break itself this drew as a misleading diagonal line back to zero rather than the near-vertical drop a real break shows. Per user instruction, each figure applies this differently: `01_controls.py`'s raw-curve Nylon 12 White figure uses `vertical_break_at_peak` (cuts at peak, appends a point at zero stress/same strain so it plots as a vertical drop, matching the other SLS batches' visual convention); `02_batch_averages.py`'s mean ± SD figure now trims **every** specimen at its peak inside `group_average` (via `truncate_at_peak`) so no fracture branch — Nylon's included — reaches the averaging grid (this replaced the old per-Nylon special-case). Both `vertical_break_at_peak` and `truncate_at_peak` are applied by the calling code, not baked into `load_standard`, since the figures need different treatments. Either way this only affects what gets plotted — the underlying JSONL `curves.strain`/`curves.stress_pa` arrays are untouched (full raw trace still there for anyone querying the dataset directly). D790 Nylon 12 White isn't affected — its curves don't show this artifact.
 
 ## Running the extract

README.md

@@ -105,12 +105,12 @@ Regenerate with `uv run scripts/plots/02_batch_averages.py`.
 
 | Config | Description | Files |
 |---|---|---|
-| `D638` (default) | Tensile specimens (ASTM D638 Type I, plus 12 Type IV specimens in batch M). 87 SLS (batches A–N) + 3 PLA + 3 PETG + 5 FormLabs PA12GF + 5 FormLabs Nylon 12 White = 103 rows. Batches A–J/J_MB have Database FKs; K–N don't yet (print jobs not backfilled). | `data/D638/*.jsonl` (one row per file) |
-| `D790` | Three-point flex specimens (ASTM D790 Procedure A). 71 SLS rows (batches C–N) + 5 FormLabs PA12GF + 5 FormLabs Nylon 12 White = 81 rows. Batches C–J/J_MB have Database FKs; K–N don't yet. | `data/D790/*.jsonl` (one row per file) |
+| `D638` (default) | Tensile specimens (ASTM D638 Type I, plus 12 Type IV specimens in batch M and Type IV Nylon 11 batches O/P). 102 SLS (batches A–P) + 3 PLA + 3 PETG + 5 FormLabs PA12GF + 5 FormLabs Nylon 12 White = 118 rows. Batches A–J/J_MB have Database FKs; K–P don't yet (print jobs not backfilled). | `data/D638/*.jsonl` (one row per file) |
+| `D790` | Three-point flex specimens (ASTM D790 Procedure A). 80 SLS rows (batches C–P) + 5 FormLabs PA12GF + 5 FormLabs Nylon 12 White = 90 rows. Batches C–J/J_MB have Database FKs; K–P don't yet. | `data/D790/*.jsonl` (one row per file) |
 
 One JSONL file per specimen — SLS rows are named after their `sample_id` (e.g. `data/D638/A1.jsonl`, `data/D790/E10.jsonl`); non-SLS controls use `{material}_TSR{n}.jsonl` (e.g. `data/D638/PLA_TSR6.jsonl`, `data/D790/PA12GF_FL_TSR1.jsonl`). Both configs share the same row schema and are produced by the per-session scripts under `scripts/specimens/`.
 
-Specimens are labeled with a `sample_id` of the form `{batch_label}{seq}` (e.g. `A1`, `C7`), where the batch label identifies the print batch they came from. Batch labels are usually a single letter, but `J` / `J_MB` are the same 2026-07-06 print batch split by post-processing: `J` specimens were tested as-printed, `J_MB` specimens were media blasted before testing. The same `sample_id` may appear in both configs — `C1` in `D638` and `C1` in `D790` are **different physical specimens** that came from the same Batch C print.
+Specimens are labeled with a `sample_id` of the form `{batch_label}{seq}` (e.g. `A1`, `C7`), where the batch label identifies the print batch they came from. Batch labels are usually a single letter, but `J` / `J_MB` are the same 2026-07-06 print batch split by post-processing: `J` specimens were tested as-printed, `J_MB` specimens were media blasted before testing. The same `sample_id` may appear in both configs — `C1` in `D638` and `C1` in `D790` are **different physical specimens** that came from the same Batch C print. Batches `O` and `P` (2026-08-03) are the first use of Nylon 11 SLS powder in this dataset — two separate prints, tested only as ASTM D638 Type IV (Batch P also has D790 flex). Their `seq` follows each batch's own lab specimen numbering rather than starting at 1: Batch O is `O10`-`O13`, and Batch P's D638 numbering skips `P7` (the xlsx export's own Test Run 7 sheet is labeled "SAMPLE 8").
 
 ## Source Layout
 
@@ -164,10 +164,13 @@ Test sessions covered:
 | `2026_07_23/flex/` | 5 | D790 | N | not yet in Database |
 | `2026_07_23/tensile/` (`tensile_nylon12white_fl.xlsx`) | 5 (NYLON12_WHITE_FL) | D638 | — (control) | n/a — benchtop comparison material |
 | `2026_07_23/flex/` (`flex_nylon12white_fl.xlsx`) | 5 (NYLON12_WHITE_FL) | D790 | — (control) | n/a — benchtop comparison material |
+| `2026_08_03/Tensile/` (`nylon11_batch1.xlsx`, Type IV) | 4 | D638 | O | not yet in Database |
+| `2026_08_03/Tensile/` (`nylon11_batch2.xlsx`, Type IV) | 11 | D638 | P | not yet in Database |
+| `2026_08_03/Flex/` (`nylon11_flex2.xlsx`) | 9 | D790 | P | not yet in Database |
 
 TSR11 in `Batch E 3pt test/` exists on disk but has empty `Data/` (aborted run, no DAQ scans) and no corresponding xlsx sheet — it is excluded from the JSONL. TSR4 in Batch I flex (`Flex 6-30/`) is excluded for a similar reason: `test_end_reason` is "Test Stopped" rather than a detected break.
 
-Batches K, L, M, and N (2026-07-15 through 2026-07-23) have no raw `TestRuns/`/h5 folders at all — only TestWorks xlsx exports were handed off, so all of these rows are `xlsx_only` (see `scripts/specimens/_lib.py`'s `build_row_from_xlsx`). Batch M's 12 Type IV specimens are a narrow-section ASTM D638 geometry (6mm × 4.15mm vs Type I's 12.8mm × 3.1mm) from the same print as its 5 Type I specimens — same `batch_label`, distinguished by `astm.type`. The FormLabs Nylon 12 White tensile control's xlsx export is a raw load/extension curve with no gauge length in the file — `strain`/`stress_pa` are derived using a user-confirmed 25mm extensometer gauge length declared in the script itself (see Composite stress–strain above); its flex counterpart derives normally via the D790 chord formulas.
+Batches K, L, M, N, O, and P (2026-07-15 through 2026-08-03) have no raw `TestRuns/`/h5 folders at all — only TestWorks xlsx exports were handed off, so all of these rows are `xlsx_only` (see `scripts/specimens/_lib.py`'s `build_row_from_xlsx`). Batch M's 12 Type IV specimens are a narrow-section ASTM D638 geometry (6mm × 4.15mm vs Type I's 12.8mm × 3.1mm) from the same print as its 5 Type I specimens — same `batch_label`, distinguished by `astm.type`. Batches O and P are entirely Type IV as well, but of a different SLS powder (Nylon 11, first use in this dataset — see `notes` on their rows) rather than a geometry variant of an existing batch, so they're excluded from the batch-average/cluster figures the same way Type IV rows always are, but get their own per-batch detail figures rather than sharing Batch M's combined Type IV figure (see `scripts/plots/_lib.py`'s `TYPE_IV_DEDICATED_BATCHES`). The FormLabs Nylon 12 White tensile control's xlsx export is a raw load/extension curve with no gauge length in the file — `strain`/`stress_pa` are derived using a user-confirmed 25mm extensometer gauge length declared in the script itself (see Composite stress–strain above); its flex counterpart derives normally via the D790 chord formulas.
 
 Batch H's 5 flex specimens (`2026_06_30/Flex 6-30/`) don't have a raw TestRuns folder — it looks like it was overwritten when the Batch I TestWorks project reused the same default `TST1.Test` name in the same directory. `flex_h_6.30.xlsx` is the only surviving record, so those 5 rows are built from that xlsx export alone: the raw load/extension curve (`curves.load_n`/`curves.extension_m`) comes from its embedded columns, but `curves.strain`/`curves.stress_pa` are empty and several `metrics` fields (`modulus_pa`, `strain_at_peak`, `strain_at_yield`, etc.) are null, since deriving them requires the support span, which this export doesn't surface. See each row's `notes` field.
 

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