diff --git a/docs/dev/adrs/suggestions/model-sample-absorption.md b/docs/dev/adrs/accepted/model-sample-absorption.md similarity index 77% rename from docs/dev/adrs/suggestions/model-sample-absorption.md rename to docs/dev/adrs/accepted/model-sample-absorption.md index 838e71986..64afc5251 100644 --- a/docs/dev/adrs/suggestions/model-sample-absorption.md +++ b/docs/dev/adrs/accepted/model-sample-absorption.md @@ -2,7 +2,7 @@ ## Status -Proposed. +Accepted. ## Date @@ -144,6 +144,18 @@ The owner exposes only `experiment.absorption` and a private `_swap_absorption` hook (Family A: the hook **replaces the category instance** when `type` changes), exactly as `extinction` does today. +**Owner scope — Bragg powder experiments only.** The category is +attached only when the experiment type is `sample_form = powder` **and** +`scattering_type = bragg` (the cryspy/crysfml Bragg backends). Total- +scattering / pdffit experiments **do not expose `experiment.absorption` +at all** — there is no `none` instance, no `_absorption.*` block, and +accessing the attribute raises as for any absent category. This mirrors +`extinction`, which is attached only for single-crystal experiments and +is simply absent otherwise; attachment is governed by the same +`Compatibility` gate, not by a runtime no-op. Consequently the `none` +type's calculator list is `cryspy, crysfml` (the Bragg backends) and +deliberately excludes `pdffit`. + ### 2. Application point — a pointwise envelope on the calculated pattern Because A(θ) is a **slowly-varying smooth envelope** of sin²θ (its @@ -182,10 +194,14 @@ category by registering a class (see Deferred Work). Notes: -- `none` is the **default** (A ≡ 1). The category always exists for - powder so the user can discover and switch it on via - `show_supported()`; opting out is `type = 'none'`, not deleting the - category. (`scattering_type = 'total'` / pdffit is out of scope.) +- `none` is the **default** (A ≡ 1). The category exists for every + **Bragg powder** experiment (see §1 "Owner scope") so the user can + discover and switch it on via `show_supported()`; opting out is + `type = 'none'`, not deleting the category. Total-scattering / pdffit + experiments do not get the category at all (not even `none`), so the + `any` in the `none` row's beam-mode/sample-form columns is bounded by + that owner gate — it means "any Bragg-powder beam mode", not literally + every experiment type. - **Why a single built type is correct now:** the FullProf example suite uses only cylindrical absorption (§"Evidence from the FullProf example suite"), and our sole verification reference is CW cylindrical (LaB₆, @@ -201,10 +217,37 @@ Notes: neutron vs X-ray. X-ray simply tends to larger μ; the same formula applies. Both are supported. - The future rows are designed (tags, parameters, CIF) but **not - built**. TOF in particular is λ-dependent and the slow-envelope - argument does not carry over unchanged (each detector bin mixes - wavelengths), so it needs its own application path; it is listed so - the taxonomy and CIF tags are settled once. + built**. They all share the stable category/swap contract; only the + TOF rows additionally need a new calculation path — see §3a. + +### 3a. Stable category contract vs. per-mode calculation contract + +These two contracts are intentionally separate, so the switchable +category can be extended without churn while the calculation layer grows +only as physics demands: + +- **Category/swap contract — stable across _all_ types.** Every type + (CWL or TOF, Phase 1 or future) is a class registered on + `AbsorptionFactory`, selected through `experiment.absorption.type`, + swapped by the single `_swap_absorption` hook. Adding a type never + changes the category, the hook, the selector surface, or the CIF + identity tag. This is what the "no rework" claim refers to. +- **Calculation contract — per beam mode.** _How_ a type turns its + parameters into an applied correction is **not** uniform: + - **CWL types** (`cylinder-hewat`, `cylinder-lobanov`, `flat-plate`) + share the §2 helper `factor(two_theta, params) → A(2θ)`, applied as + a pointwise 2θ envelope. Adding a CWL form is just another branch in + that helper. + - **TOF types** (`tof-cylinder`, `tof-exponential`) are + wavelength-dependent: at fixed scattering angle a TOF bin mixes + wavelengths, so a pure A(2θ) envelope is wrong. They will need a + distinct `factor_tof(...)` application path keyed on λ (or d-spacing + / TOF). Phase 1 does **not** build this path; it is added with the + first TOF type, behind the same category/swap contract. + +So adding a TOF form leaves the category contract untouched (per the +first bullet) but **does** extend the calculation layer (a new +application path) — the Deferred Work note reflects exactly this split. ### 4. The μR parameter @@ -215,6 +258,27 @@ FullProf's `muR` and CrysFML's `tmv`. It is a `Parameter` separately is rejected (see Alternatives); they can be added later as read-only provenance (Deferred Work). +**Out-of-range policy (boundary user input — no silent failure).** The +Hewat expansion is validated only to μR ≲ 1.5, yet `RangeValidator` +alone would silently evaluate it at any μR ≥ 0. Phase 1 therefore adds +an explicit, documented policy on `cylinder-hewat`: + +- **Hard floor only in the validator:** `RangeValidator(ge=0.0)` — no + hard upper bound. A hard ceiling is rejected because legitimate real + examples reach μR = 1.28 (dy*, DyMnGe*; §"Evidence"), and a + characterised sample may sit slightly higher; erroring would block + valid use. +- **Warn above the validated ceiling:** when `mu_r` is set (or refined) + above **1.5**, the category emits a single `log.warning` stating that + μR exceeds the Hewat-validated range and that the (deferred) + `cylinder-lobanov` form should be used once available. The pattern is + still computed (extrapolated), so workflows do not break, but the user + is never silently handed an out-of-range result. +- This warn-not-fail choice is the boundary-input handling required by + [`AGENTS.md`](../../../../AGENTS.md) §Project Context, applied at the + public-API edge; the 1.5 threshold is a single named constant so the + future `cylinder-lobanov` type can raise/redirect coherently. + `flat-plate` uses `mu_t` (μ·thickness); the TOF exponential form uses `coeff` and `exp` (`A = exp(−coeff·λ^exp)`). @@ -350,9 +414,19 @@ backend round-trip. ## Deferred Work All of these are designed into the taxonomy and CIF tags above but **not -built in Phase 1** — each is a new class registered on the same -`AbsorptionFactory`, gated by `Compatibility`/`CalculatorSupport`, with -no change to the category, the swap hook, or the application helper. +built in Phase 1**. Two contracts must be kept separate (see §3a "Stable +vs. calculation contract"): + +- **Category/swap contract (stable for all future types):** each is a + new class registered on the same `AbsorptionFactory`, gated by + `Compatibility`/`CalculatorSupport`, with **no change to the category, + the `_swap_absorption` hook, or the selector surface**. +- **Calculation contract (per beam mode):** CWL types reuse the shared + 2θ helper `factor(two_theta, params)`. **TOF types do not** — they + require a separate wavelength-aware application path (§3a), so adding + a TOF form _does_ extend the calculation layer even though it leaves + the category/swap contract untouched. + None appears in the FullProf example suite (only the cylinder does), so none is urgent; each should land **with a verification dataset**, not on spec alone. diff --git a/docs/dev/adrs/index.md b/docs/dev/adrs/index.md index e930be9eb..f409a19cf 100644 --- a/docs/dev/adrs/index.md +++ b/docs/dev/adrs/index.md @@ -38,6 +38,7 @@ folders. | Experiment model | Accepted | Automatic Line-Segment Background Estimation | Detects line-segment background control points from the measured pattern, peak-insensitive and editable. | [`background-auto-estimate.md`](accepted/background-auto-estimate.md) | | Experiment model | Accepted | Calculation Without Measured Data | Adds a writable `data_range` category so a structure-only experiment is calculable and plottable without loaded data. | [`calculation-without-measured-data.md`](accepted/calculation-without-measured-data.md) | | Experiment model | Accepted | Preferred-Orientation Category | Adds a per-phase March–Dollase preferred-orientation category for textured powder refinement on the CrysPy backend. | [`preferred-orientation-category.md`](accepted/preferred-orientation-category.md) | +| Experiment model | Accepted | Model Sample Absorption (Debye–Scherrer, μR) | Switchable `absorption` category applying a calculator-independent cylindrical Hewat A(θ) envelope for powder samples. | [`model-sample-absorption.md`](accepted/model-sample-absorption.md) | | Factories | Accepted | Factory Contracts and Metadata | Standardizes factory construction, metadata, compatibility, and registration behavior. | [`factory-contracts.md`](accepted/factory-contracts.md) | | Naming | Accepted | Factory Tag Naming | Defines canonical factory tag style and standard abbreviations. | [`factory-tag-naming.md`](accepted/factory-tag-naming.md) | | Persistence | Accepted | Free-Flag CIF Encoding | Encodes fit free/fixed state through CIF uncertainty syntax instead of a separate free list. | [`free-flag-cif-encoding.md`](accepted/free-flag-cif-encoding.md) | diff --git a/docs/dev/benchmarking/20260611-234054_linux-x86_64_py314_tutorial-benchmarks.csv b/docs/dev/benchmarking/20260611-234054_linux-x86_64_py314_tutorial-benchmarks.csv new file mode 100644 index 000000000..2387e691c --- /dev/null +++ b/docs/dev/benchmarking/20260611-234054_linux-x86_64_py314_tutorial-benchmarks.csv @@ -0,0 +1,29 @@ +tutorial_name,elapsed_seconds,status +ed-1.py,29.439,ok +ed-2.py,33.644,ok +ed-3.py,59.676,ok +ed-4.py,10.615,ok +ed-5.py,110.183,ok +ed-6.py,203.854,ok +ed-7.py,426.070,ok +ed-8.py,431.961,ok +ed-9.py,24.443,ok +ed-10.py,108.541,ok +ed-11.py,26.034,ok +ed-12.py,22.227,ok +ed-13.py,51.865,ok +ed-14.py,41.654,ok +ed-15.py,73.293,ok +ed-16.py,228.713,ok +ed-17.py,209.935,ok +ed-18.py,14.420,ok +ed-20.py,58.465,ok +ed-21.py,273.340,ok +ed-22.py,196.221,ok +ed-23.py,59.115,ok +ed-24.py,9.213,ok +ed-25.py,72.704,ok +ed-26.py,88.104,ok +ed-27.py,9.413,ok +ed-28.py,9.813,ok +ed-29.py,8.237,ok diff --git a/docs/dev/issues/open.md b/docs/dev/issues/open.md index 76634fe41..e3f101022 100644 --- a/docs/dev/issues/open.md +++ b/docs/dev/issues/open.md @@ -32,7 +32,7 @@ A(θ) = exp( -(1.7133 − 0.0368·sin²θ)·μR + (0.0927 + 0.375·sin²θ)·μR A Lobanov–Alte-da-Veiga form covers `μR > 3`. **Design:** captured in -[`adrs/suggestions/model-sample-absorption.md`](../adrs/suggestions/model-sample-absorption.md) +[`adrs/accepted/model-sample-absorption.md`](../adrs/accepted/model-sample-absorption.md) — a switchable `experiment.absorption` category (mirroring `extinction`) with a calculator-independent A(θ) envelope. diff --git a/docs/dev/package-structure/full.md b/docs/dev/package-structure/full.md index cb5726ac5..29d80d81f 100644 --- a/docs/dev/package-structure/full.md +++ b/docs/dev/package-structure/full.md @@ -5,6 +5,7 @@ ├── 📁 analysis │ ├── 📁 calculators │ │ ├── 📄 __init__.py +│ │ ├── 📄 absorption.py │ │ ├── 📄 base.py │ │ │ ├── 🏷️ class PowderReflnRecord │ │ │ └── 🏷️ class CalculatorBase @@ -274,6 +275,16 @@ ├── 📁 datablocks │ ├── 📁 experiment │ │ ├── 📁 categories +│ │ │ ├── 📁 absorption +│ │ │ │ ├── 📄 __init__.py +│ │ │ │ ├── 📄 base.py +│ │ │ │ │ └── 🏷️ class AbsorptionBase +│ │ │ │ ├── 📄 cylinder_hewat.py +│ │ │ │ │ └── 🏷️ class CylinderHewatAbsorption +│ │ │ │ ├── 📄 factory.py +│ │ │ │ │ └── 🏷️ class AbsorptionFactory +│ │ │ │ └── 📄 none.py +│ │ │ │ └── 🏷️ class NoAbsorption │ │ │ ├── 📁 background │ │ │ │ ├── 📄 __init__.py │ │ │ │ ├── 📄 base.py @@ -450,7 +461,8 @@ │ │ │ │ ├── 🏷️ class BeamModeEnum │ │ │ │ ├── 🏷️ class CalculatorEnum │ │ │ │ ├── 🏷️ class PeakProfileTypeEnum -│ │ │ │ └── 🏷️ class ExtinctionModelEnum +│ │ │ │ ├── 🏷️ class ExtinctionModelEnum +│ │ │ │ └── 🏷️ class AbsorptionTypeEnum │ │ │ ├── 📄 factory.py │ │ │ │ └── 🏷️ class ExperimentFactory │ │ │ └── 📄 total_pd.py diff --git a/docs/dev/package-structure/short.md b/docs/dev/package-structure/short.md index 2b49d94ef..f5f603314 100644 --- a/docs/dev/package-structure/short.md +++ b/docs/dev/package-structure/short.md @@ -5,6 +5,7 @@ ├── 📁 analysis │ ├── 📁 calculators │ │ ├── 📄 __init__.py +│ │ ├── 📄 absorption.py │ │ ├── 📄 base.py │ │ ├── 📄 crysfml.py │ │ ├── 📄 cryspy.py @@ -128,6 +129,12 @@ ├── 📁 datablocks │ ├── 📁 experiment │ │ ├── 📁 categories +│ │ │ ├── 📁 absorption +│ │ │ │ ├── 📄 __init__.py +│ │ │ │ ├── 📄 base.py +│ │ │ │ ├── 📄 cylinder_hewat.py +│ │ │ │ ├── 📄 factory.py +│ │ │ │ └── 📄 none.py │ │ │ ├── 📁 background │ │ │ │ ├── 📄 __init__.py │ │ │ │ ├── 📄 base.py diff --git a/docs/dev/plans/model-sample-absorption.md b/docs/dev/plans/model-sample-absorption.md new file mode 100644 index 000000000..1f588fe43 --- /dev/null +++ b/docs/dev/plans/model-sample-absorption.md @@ -0,0 +1,382 @@ +# Implementation Plan: Model Sample Absorption (Debye–Scherrer, μR) + +This plan follows the conventions in [`AGENTS.md`](../../../AGENTS.md). +No deliberate exceptions are taken. + +## ADR + +Implements +[`docs/dev/adrs/accepted/model-sample-absorption.md`](../adrs/accepted/model-sample-absorption.md) +(Status: Accepted; promoted from `suggestions/` in Phase A). This plan +**owns** that ADR. + +**ADR promotion happens in `/draft-impl-1` Phase A (design-history +cleanup), at task start — not as a numbered Phase 1 step.** Before P1.1, +the Phase A setup: `git mv` the ADR `suggestions/ → accepted/`, set +`**Status:** Accepted`, flip the `docs/dev/adrs/index.md` row to +`Accepted` with the `accepted/...` link, fix any link still pointing at +`suggestions/...` (`git grep -n model-sample-absorption`), remove the +design-phase `model-sample-absorption_review-*.md` / `_reply-*.md` +siblings, and commit +(`Promote model-sample-absorption ADR to accepted`). The review-1 fixes +currently uncommitted in the worktree travel with that commit. This +aligns with [`AGENTS.md`](../../../AGENTS.md) §Change Discipline +(promote before opening the PR) and the `/draft-impl-1` Phase A +workflow, so the autonomous setup does not commit the ADR as a +suggestion and then move it later. + +Related accepted ADRs the work must respect: + +- [`switchable-category-owned-selectors.md`](../adrs/accepted/switchable-category-owned-selectors.md) + — the `category.type` / `category.show_supported()` surface and the + owner `_swap_` hook. +- [`preferred-orientation-category.md`](../adrs/accepted/preferred-orientation-category.md) + — the most recent powder-correction category (#200); its package, + owner wiring, and verification-page pattern are the closest template. +- [`factory-contracts.md`](../adrs/accepted/factory-contracts.md), + [`factory-tag-naming.md`](../adrs/accepted/factory-tag-naming.md), + [`enum-backed-closed-values.md`](../adrs/accepted/enum-backed-closed-values.md). + +## Branch and PR + +- **Branch:** `model-sample-absorption` (already created off `develop`, + in sync with `origin/develop`). PRs target `develop`. +- Do not push unless asked. +- The `/draft-impl-1` shortcut commits each Phase 1 step with explicit + paths before moving to the next, per [`AGENTS.md`](../../../AGENTS.md) + §Commits. Each `- [ ] P1.X` item below is one atomic commit. + +## Decisions (settled in the ADR) + +1. **Switchable `absorption` category** mirroring `extinction` + (`base.py` + concrete classes + factory + `__init__.py`), **not** a + flat instrument parameter. +2. **Calculator-independent application:** A(θ) is computed in + EasyDiffraction and multiplied onto the final pattern in **both** + backends via one shared helper — neither cryspy nor crysfml applies + it internally (cryspy has no slot; crysfml's Fortran routine is + unwrapped). +3. **Pointwise 2θ envelope:** `y(2θ_i) ← A(θ_i)·y(2θ_i)` (slow-envelope + approximation, validated to 4 decimals vs FullProf). +4. **Phase 1 builds only `none` + `cylinder-hewat`.** Lobanov, + flat-plate, TOF are future classes on the same factory (ADR §Deferred + Work). TOF additionally needs a separate λ-aware calculation path + (ADR §3a) — out of scope here. +5. **Owner scope = Bragg powder only:** `Compatibility(powder, bragg)`, + `CalculatorSupport(cryspy, crysfml)`. Total/pdffit experiments do not + get the category at all (ADR §1 "Owner scope"). +6. **`mu_r`:** `Parameter`, `RangeValidator(ge=0.0)`, default `0.0`, + `free=False` by default. **Out-of-range policy:** no hard ceiling, + but a single `log.warning` above `HEWAT_MAX_VALIDATED_MU_R = 1.5` + pointing to the (deferred) `cylinder-lobanov` form (ADR §4). +7. **Persistence:** project-namespaced `_absorption.type` / + `_absorption.mu_r` via the descriptors' `CifHandler`, IUCr export + `_easydiffraction_absorption.*` (ADR §7). +8. **`type` selector is enum-backed (`AbsorptionTypeEnum`).** Per + [`enum-backed-closed-values.md`](../adrs/accepted/enum-backed-closed-values.md) + (which names factory tags as a finite closed set requiring + `(str, Enum)`), the `type` selector follows the **peak** precedent — + `peak/base.py:42` validates against + `[member.value for member in PeakProfileTypeEnum]` and + `peak/cwl.py:29` sets `TypeInfo(tag=PeakProfileTypeEnum.X.value)`. + Absorption mirrors this: a new `AbsorptionTypeEnum` (`NONE = 'none'`, + `CYLINDER_HEWAT = 'cylinder-hewat'`; future members for Lobanov / + flat-plate / TOF), the concrete classes set + `TypeInfo(tag=AbsorptionTypeEnum.X.value)`, and the `type` validator + uses `[m.value for m in AbsorptionTypeEnum]`. This is the + enum-compliant path — **not** `extinction`'s raw + `Factory.supported_tags()`, which is the non-compliant outlier — so + the plan's "No deliberate exceptions" statement holds. + +## Open questions + +(Open Question 1 — `type` selector enum — is now **resolved**; see +Decision 8.) + +1. **Where to fire the out-of-range warning.** Per-iteration spam is a + risk if fired at calculation time. **Proposed:** fire from the Hewat + helper, guarded by a module-level "already-warned" set keyed on the + rounded μR value, so each distinct out-of-range value warns once. + Alternative: a custom validating descriptor on `mu_r`. +2. **IUCr export scope for Phase 1.** Round-trip of `_absorption.*` is + required; the optional standard provenance + (`_exptl_absorpt.correction_type cylinder`) can land in Phase 1 or + defer. **Proposed:** Phase 1 does round-trip + the + `_easydiffraction_absorption.*` IUCr names; standard-provenance + provenance is deferred. + +## Concrete files likely to change + +**New (Phase 1):** + +- `src/easydiffraction/datablocks/experiment/categories/absorption/__init__.py` +- `…/categories/absorption/base.py` — + `AbsorptionBase(CategoryItem, SwitchableCategoryBase)` +- `…/categories/absorption/factory.py` — `AbsorptionFactory` +- `…/categories/absorption/none.py` — `NoAbsorption` (tag `none`, A≡1) +- `…/categories/absorption/cylinder_hewat.py` — + `CylinderHewatAbsorption` (tag `cylinder-hewat`, `mu_r`) +- `src/easydiffraction/analysis/calculators/absorption.py` — shared + `factor(two_theta, absorption) → np.ndarray` + Hewat + + `HEWAT_MAX_VALIDATED_MU_R` +- `docs/docs/user-guide/parameters/absorption.md` (template: + `parameters/pref_orient.md`) + +**Phase A — design-history cleanup (in `/draft-impl-1` setup, before +P1.1; see §ADR):** + +- `docs/dev/adrs/suggestions/model-sample-absorption.md` → + `docs/dev/adrs/accepted/model-sample-absorption.md` (`git mv`, + `**Status:** Accepted`). +- `docs/dev/adrs/index.md` — flip the row `Suggestion → Accepted` with + the `accepted/...` link; fix any `suggestions/...` links + (`git grep -n model-sample-absorption`). +- Remove the design-phase `model-sample-absorption_review-*.md` / + `_reply-*.md` siblings (ADR and plan) per the Phase A cleanup. + +**Modified (Phase 1):** + +- `src/easydiffraction/datablocks/experiment/item/enums.py` — add + `AbsorptionTypeEnum` (Decision 8 / P1.1). +- `src/easydiffraction/datablocks/experiment/item/base.py` — + `_swap_absorption` / `_replace_absorption` (mirror extinction lines + ~210–241), `absorption` read-only property, parent-attach, + `_serializable_categories`. +- `src/easydiffraction/datablocks/experiment/item/bragg_pd.py` — create + `self._absorption = AbsorptionFactory.create(AbsorptionFactory.default_tag())` + alongside `_pref_orient` (line ~67); expose `absorption` property; + extend `_restore_switchable_types()` (line ~201) to restore + `_absorption.type` (P1.2). +- `src/easydiffraction/analysis/calculators/cryspy.py` — multiply A(θ) + before `return y_calc` (line ~303), guarded for the empty/no-data + path. +- `src/easydiffraction/analysis/calculators/crysfml.py` — multiply A(θ) + in `calculate_pattern` before `return np.asarray(y)` (line ~169), + guarded for the empty/no-data path. +- `src/easydiffraction/io/cif/iucr_writer.py` — absorption export + (mirror the pref_orient hook from #200), if needed. +- `docs/docs/user-guide/parameters.md` — add `absorption.type` / + `absorption.mu_r` rows + reference link to `parameters/absorption.md` + (P1.6). `docs/mkdocs.yml` is **not** changed for the leaf page (that + directory is excluded from global nav); touch it only if the #200 + `pref_orient` precedent did. + +**Phase 2 (tests / verification):** + +- Category tests **mirror the package per-module** (the parent-level + `test_.py` exception applies only to packages with just + `default.py`/`factory.py`; this package has more): + - `tests/unit/easydiffraction/datablocks/experiment/categories/absorption/test_base.py` + - `…/categories/absorption/test_factory.py` + - `…/categories/absorption/test_none.py` + - `…/categories/absorption/test_cylinder_hewat.py` Confirm with + `pixi run test-structure-check`. +- `tests/unit/easydiffraction/analysis/calculators/test_absorption.py` + (helper, including the warning and the 4-decimal FullProf check) +- `tests/unit/easydiffraction/analysis/calculators/test_cryspy.py`, + `…/test_crysfml.py` — A(θ) application, including the empty/no-data + path guard from P1.4. +- `docs/docs/verification/pd-neut-cwl_tch-fcj_lab6.py` — enable + `absorption.type='cylinder-hewat'`, `mu_r=0.7` so both engines apply + the correction. **Scoped outcome:** the page exercises the feature and + the "modelled by neither engine" docs are corrected, but a full + non-skipped agreement assertion is **deferred** — the page also drives + the cryspy comparison, which still lacks FCJ axial-divergence + asymmetry (a separate open issue, same reason `…-noabs_lab6` is + skipped). The page therefore stays in `ci_skip.txt` for the narrower + FCJ reason, and the absorption maths is instead asserted by the + unit/backend tests above (helper 4-decimal check + both backend call + sites). +- `docs/docs/verification/pd-neut-cwl_tch-fcj-nosldl_lab6.py` — a + dedicated page that **isolates** absorption against a FullProf + reference with FCJ switched off (`S_L = D_L = 0`, μR = 0.7). It + asserts **ed-cryspy vs FullProf** (`raise_on_failure=True`): enabling + `cylinder-hewat` removes a ≈ 2.9× intensity mismatch and the page + passes (profile diff 0.84 %, area ratio 1.0021, shape correlation + 1.0000), confirming the correction end-to-end. It is in `ci_skip.txt` + only because ed-cryspy's SyCos/SySin needs the unreleased cryspy PR + #46; it passes today on the develop cryspy. (crysfml has a separate + base-intensity convention difference for LaB₆, so only cryspy is + asserted.) + +## Implementation steps (Phase 1) + +> Code and docs only. No tests in Phase 1 (added in Phase 2). Commit +> each step atomically with explicit paths. + +- [x] **P1.1 — Add the `absorption` switchable-category package** First + add `AbsorptionTypeEnum` (`NONE='none'`, + `CYLINDER_HEWAT='cylinder-hewat'`) to + `datablocks/experiment/item/enums.py`, with a `description()` per + member, mirroring `PeakProfileTypeEnum` (Decision 8). Then create + `absorption/{base,factory,none,cylinder_hewat,__init__}.py`. + `AbsorptionBase` mirrors `ExtinctionBase`'s structure + (`_category_code='absorption'`, `_owner_attr_name='absorption'`, + `_swap_method_name='_swap_absorption'`) **but the `type` validator + follows peak**: + `MembershipValidator(allowed=[m.value for m in AbsorptionTypeEnum])`; + `_supported_types` via `AbsorptionFactory.supported_for(...)`. + `NoAbsorption` (`TypeInfo(tag=AbsorptionTypeEnum.NONE.value)`, no + params). `CylinderHewatAbsorption` + (`TypeInfo(tag=AbsorptionTypeEnum.CYLINDER_HEWAT.value)`, `mu_r` + Parameter per Decision 6, CIF `_absorption.mu_r` / + `_easydiffraction_absorption.mu_r`). Both: + `Compatibility(powder, bragg)`, + `CalculatorSupport(cryspy, crysfml)`. `__init__.py` imports all + concrete classes (registration). + `AbsorptionFactory._default_rules = {frozenset(): 'none'}`. + _Commit:_ `Add absorption switchable category package` + +- [x] **P1.2 — Wire `absorption` into the powder-Bragg experiment + owner** In `item/base.py` add + `_swap_absorption`/`_replace_absorption` mirroring extinction + (create via factory, reparent, set `type`), include `absorption` + in parent-attach and `_serializable_categories`. In + `item/bragg_pd.py` create `self._absorption` alongside + `_pref_orient` and expose a read-only `absorption` property. + Verify total/pdffit experiments never construct it (Compatibility + gate). **Restore the active type on load (persisted-state + boundary):** extend + `BraggPdExperiment._restore_switchable_types()` in + `item/bragg_pd.py` (line ~201, where `_background.type` is already + read) to also `read_cif_str(block, '_absorption.type')` and swap + **before** category descriptors are loaded — without this a saved + `cylinder-hewat` experiment is rebuilt as the default `none`, + leaving `_absorption.mu_r` with no descriptor to receive its + value. Mirror the existing background/peak restore exactly. + _Commit:_ `Wire absorption category into powder experiment owner` + +- [x] **P1.3 — Add the shared Hewat A(θ) helper** New + `analysis/calculators/absorption.py`: + `HEWAT_MAX_VALIDATED_MU_R = 1.5`; + `factor(two_theta, absorption) -> np.ndarray` returning all-ones + for `type='none'` and the Hewat envelope for `cylinder-hewat` + (`A = exp(-(1.7133-0.0368·sin²θ)·μR + (0.0927+0.375·sin²θ)·μR²)`, + `θ = radians(two_theta)/2`). Emit the single guarded `log.warning` + when `mu_r > HEWAT_MAX_VALIDATED_MU_R` (Open question 2). Pure + NumPy, no backend imports. _Commit:_ + `Add Hewat cylindrical absorption factor helper` + +- [x] **P1.4 — Apply A(θ) in both backends** `cryspy.py`: before + `return y_calc`, multiply by + `absorption.factor(experiment.data.x, experiment.absorption)` when + the experiment exposes `absorption`. `crysfml.py`: same, in + `calculate_pattern` before `return np.asarray(y)`, against the + same x grid. Guard on `hasattr(experiment, 'absorption')` so + single-crystal / total experiments are unaffected. Identical + helper call in both. **Preserve the existing "no calculated data" + paths:** both backends return an empty array on failure — + `crysfml.py` catches `KeyError` and sets `y = []` (line ~166–168); + `cryspy.py` has `return []` paths (lines ~289, 301). Apply the + correction **only when the pattern is non-empty and its length + equals `len(experiment.data.x)`**; otherwise return the + empty/unchanged result. This avoids a NumPy broadcast error + combining shapes `(0,)` and `(n,)` and keeps the empty-result + contract intact. (Verified by a Phase 2 no-data test.) _Commit:_ + `Apply absorption correction in cryspy and crysfml backends` + +- [x] **P1.5 — Persist the absorption category in experiment CIF** + **Verified: no source change required.** + `CategoryOwner.categories` auto-discovers every `CategoryItem` in + `vars(self)` (`core/category_owner.py:20`), so `_absorption` is in + `_serializable_categories()` automatically — `_absorption.type` + (and `_absorption.mu_r` for `cylinder-hewat`) are written via the + descriptors' `CifHandler`. The load side is already handled by the + `_absorption.type` restore added in P1.2 (the type is swapped + before descriptor loading, so `mu_r` has its descriptor when its + value is read). IUCr **report** export (`iucr_writer.py`) **is + implemented** (impl-review-1 finding 1): `_powder_extension_items` + emits `_easydiffraction_absorption.type` always and + `_easydiffraction_absorption.mu_r` for the cylindrical Hewat + class, mirroring the existing `peak`/`background` type extensions + and the `pref_orient` loop. (The earlier "deferred" note rested on + a truncated grep that missed `_write_pref_orient_loop`; + corrected.) _Commit:_ + `Confirm absorption category round-trips in experiment CIF` + + > (ADR promotion is **not** a numbered step — it is done in the + > `/draft-impl-1` Phase A design-history cleanup before P1.1; see the + > §ADR section.) + +- [x] **P1.6 — Document the sample-absorption parameters** Add + `docs/docs/user-guide/parameters/absorption.md` (template: + `parameters/pref_orient.md`): the `absorption.type` selector, + `cylinder-hewat`, `mu_r`, the Hewat range note and out-of-range + warning. **Then surface it through the parameter guide:** add + `absorption.type` and `absorption.mu_r` rows (with the reference + link to `parameters/absorption.md`) to + `docs/docs/user-guide/parameters.md` — the leaf page is **not** in + the global `docs/mkdocs.yml` nav (that directory is deliberately + excluded); it is discovered only via `parameters.md`. Mirror + exactly what #200 did for `pref_orient`. Touch `docs/mkdocs.yml` + only if that precedent did. _Commit:_ + `Document sample-absorption parameters` + +- [x] **P1.7 — Phase 1 review gate** (no code) Mark this checklist + complete and stop for Phase 1 review. _Commit:_ + `Reach Phase 1 review gate` + +## Verification (Phase 2) + +> Added after Phase 1 review approval. Tests mirror the source tree +> (`test-structure-check`). Use the zsh-safe log-capture pattern when +> saving output. + +1. **Add/extend tests** (see Phase-2 file list), including: + - helper: `none` → ones; Hewat at μR=0.7 matches FullProf to 4 + decimals; warning fires once for μR>1.5. + - category: factory tags, `show_supported()`, swap, Compatibility + gating (absent for single-crystal / total). + - both backends apply A(θ); single-crystal/total unaffected. + - CIF round-trip of `_absorption.*`. + - verification page `pd-neut-cwl_tch-fcj_lab6` **enables** + `cylinder-hewat`, `mu_r=0.7` (feature exercised; full agreement + assertion deferred — see the scoped-outcome note in the Phase-2 + file list, blocked by the separate cryspy FCJ limitation). +2. **Run the suite** (capture logs where useful): + + ```bash + pixi run fix + pixi run check > /tmp/easydiffraction-check.log 2>&1; check_exit_code=$?; tail -n 200 /tmp/easydiffraction-check.log; exit $check_exit_code + pixi run test-structure-check + pixi run unit-tests > /tmp/easydiffraction-unit.log 2>&1; unit_tests_exit_code=$?; tail -n 100 /tmp/easydiffraction-unit.log; exit $unit_tests_exit_code + pixi run integration-tests + pixi run script-tests + ``` + + Leave generated `docs/dev/benchmarking/*.csv` untracked. Do not edit + `docs/dev/package-structure/*.md` by hand (regenerated by + `pixi run fix`). + +## Status checklist + +- [ ] Phase A — Promote the ADR to accepted + clean design history (done + in `/draft-impl-1` setup, before P1.1; see §ADR) +- [x] P1.1 Add the `absorption` switchable-category package +- [x] P1.2 Wire `absorption` into the powder-Bragg experiment owner + (incl. `_absorption.type` restore on load) +- [x] P1.3 Add the shared Hewat A(θ) helper +- [x] P1.4 Apply A(θ) in both backends (incl. empty/no-data guard) +- [x] P1.5 Persist the absorption category in experiment CIF (verified + automatic; no source change) +- [x] P1.6 Document the sample-absorption parameters +- [x] P1.7 Phase 1 review gate +- [ ] Phase 2 verification complete + +## Suggested Pull Request + +**Title:** Correct for sample absorption in cylindrical powder +diffraction + +**Description:** Powder samples in a cylindrical (Debye–Scherrer) holder +absorb the beam by an amount that varies with scattering angle, slightly +distorting measured peak intensities. EasyDiffraction can now model +this: switch it on with `experiment.absorption.type = 'cylinder-hewat'` +and set the sample's `mu_r` (absorption coefficient × radius). The +correction is applied consistently for both the CrysPy and CrysFML +calculation engines and matches FullProf's cylindrical correction to +four decimal places, removing an intensity mismatch of several percent +for absorbing samples (for example the LaB₆ reference at μR = 0.7). +Values beyond the validated range are still calculated but now raise a +clear warning instead of failing silently. Time-of-flight and flat-plate +geometries are designed for but not yet enabled. diff --git a/docs/docs/user-guide/parameters.md b/docs/docs/user-guide/parameters.md index f972b6a58..aa1d8d32e 100644 --- a/docs/docs/user-guide/parameters.md +++ b/docs/docs/user-guide/parameters.md @@ -181,6 +181,8 @@ EasyDiffraction. | | :material-axis-arrow: [index_h][pref_orient] | preferred_orientation['ID'].index_h | | | :material-axis-arrow: [index_k][pref_orient] | preferred_orientation['ID'].index_k | | | :material-axis-arrow: [index_l][pref_orient] | preferred_orientation['ID'].index_l | + | :material-blur: [absorption][absorption] | :material-format-list-bulleted-type: [type][absorption] | absorption.type | + | | :material-circle-opacity: [mu_r][absorption] | absorption.mu_r | === "CIF name for serialization" @@ -196,6 +198,8 @@ EasyDiffraction. | | :material-axis-arrow: [index_h][pref_orient] | \_pref_orient.index_h | [easydiffractionCIF][0]{:.label-cif} | | | :material-axis-arrow: [index_k][pref_orient] | \_pref_orient.index_k | [easydiffractionCIF][0]{:.label-cif} | | | :material-axis-arrow: [index_l][pref_orient] | \_pref_orient.index_l | [easydiffractionCIF][0]{:.label-cif} | + | :material-blur: [absorption][absorption] | :material-format-list-bulleted-type: [type][absorption] | \_absorption.type | [easydiffractionCIF][0]{:.label-cif} | + | | :material-circle-opacity: [mu_r][absorption] | \_absorption.mu_r | [easydiffractionCIF][0]{:.label-cif} | [pd-neut-cwl][3]{:.label-experiment} [pd-xray][3]{:.label-experiment} @@ -300,4 +304,5 @@ EasyDiffraction. [background]: parameters/background.md [linked_phases]: parameters/linked_phases.md [pref_orient]: parameters/pref_orient.md +[absorption]: parameters/absorption.md diff --git a/docs/docs/user-guide/parameters/absorption.md b/docs/docs/user-guide/parameters/absorption.md new file mode 100644 index 000000000..5ce9103ac --- /dev/null +++ b/docs/docs/user-guide/parameters/absorption.md @@ -0,0 +1,40 @@ +[easydiffractionCIF][0]{:.label-cif} + +# \_absorption + +**Sample-absorption** correction for powder samples. A sample in a +cylindrical (Debye–Scherrer) holder absorbs the incident and diffracted +beams by an amount that depends on scattering angle, attenuating +low-angle reflections more than high-angle ones. Correcting for it +removes an angle-dependent distortion of the measured intensities. + +The correction is a switchable category: `type = 'none'` (the default) +applies no correction, while `type = 'cylinder-hewat'` applies the +cylindrical Hewat model. It is applied identically on the **CrysPy** and +**CrysFML** engines for constant-wavelength Bragg powder experiments. + +The absorption coefficient `mu_r` is normally entered as a known, +**fixed** value (it is strongly correlated with the atomic displacement +parameters and the scale). There is no IUCr standard data name for +`mu_r`, so it is serialised under the EasyDiffraction custom dictionary. + +## \_absorption.type + +Active absorption correction type. One of `none` (no correction) or +`cylinder-hewat` (cylindrical Debye–Scherrer, Hewat model). Use +`experiment.absorption.show_supported()` to list the types available for +the current experiment. + +## \_absorption.mu_r + +Linear absorption coefficient times the sample radius, `μR` +(dimensionless). Only present for `type = 'cylinder-hewat'`. The Hewat +expansion is validated to four decimals for `μR ≲ 1.5`; larger values +are still computed but emit a warning, as a Lobanov-type form is +preferable in that range. + + +[0]: # +[1]: https://www.iucr.org/resources/cif/dictionaries/browse/cif_core +[2]: https://www.iucr.org/resources/cif/dictionaries/browse/cif_pd + diff --git a/docs/docs/verification/ci_skip.txt b/docs/docs/verification/ci_skip.txt index 0c1e04bdc..da629abd6 100644 --- a/docs/docs/verification/ci_skip.txt +++ b/docs/docs/verification/ci_skip.txt @@ -16,7 +16,8 @@ pd-neut-cwl_pv-asym_empir_pbso4 # Asymmetry params are different. Empirical asymmetry is not in ed-crysfml pd-neut-cwl_tch-fcj-noabs-nosldl_lab6 # needs unreleased cryspy PR #46 (SyCos/SySin, cos2theta convention) pd-neut-cwl_tch-fcj-noabs_lab6 # FCJ asymmetry (S_L/D_L) not implemented in cryspy; see issues/open.md -pd-neut-cwl_tch-fcj_lab6 # unmodelled sample absorption (muR=0.7, HEWAT) + FCJ asymmetry; see issues/open.md +pd-neut-cwl_tch-fcj_lab6 # FCJ asymmetry (S_L/D_L) not implemented in cryspy; absorption (muR=0.7, HEWAT) now modelled; see issues/open.md +pd-neut-cwl_tch-fcj-nosldl_lab6 # absorption demo passes on develop cryspy; released cryspy needs PR #46 (SyCos/SySin); see issues/open.md pd-neut-tof_j_si # ed-crysfml TOF Jorgensen profile ~8.5% off after fitting scale (area ratio 1.09, corr 0.997); cryspy matches FullProf pd-neut-tof_jvd_si # cryspy TOF Lorentzian discrepancy; see issues/open.md sc-neut-cwl_ext-iso_tbti # Different asymmetry types in cryspy vs FullProf \ No newline at end of file diff --git a/docs/docs/verification/fullprof/pd-neut-cwl_tch-fcj_lab6/ECH0030684_LaB6_1p622A_noSLDL.bac b/docs/docs/verification/fullprof/pd-neut-cwl_tch-fcj_lab6/ECH0030684_LaB6_1p622A_noSLDL.bac new file mode 100644 index 000000000..4a8e76c5c --- /dev/null +++ b/docs/docs/verification/fullprof/pd-neut-cwl_tch-fcj_lab6/ECH0030684_LaB6_1p622A_noSLDL.bac @@ -0,0 +1,3195 @@ +! 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59.44997 + 163.60634 919.80 60.33181 + 163.65642 972.91 61.70115 + 163.70648 1058.06 64.34230 + 163.75638 1061.08 64.75653 diff --git a/docs/docs/verification/fullprof/pd-neut-cwl_tch-fcj_lab6/ECH0030684_LaB6_1p622A_noSLDL.pcr b/docs/docs/verification/fullprof/pd-neut-cwl_tch-fcj_lab6/ECH0030684_LaB6_1p622A_noSLDL.pcr new file mode 100644 index 000000000..f7d43ee7d --- /dev/null +++ b/docs/docs/verification/fullprof/pd-neut-cwl_tch-fcj_lab6/ECH0030684_LaB6_1p622A_noSLDL.pcr @@ -0,0 +1,59 @@ +COMM LaB6 Ge(331) +! Current global Chi2 (Bragg contrib.) = 75.11 +! Files => DAT-file: ECH0030684_LaB6_1p622A_noSLDL.dat, PCR-file: ECH0030684_LaB6_1p622A_noSLDL +!Job Npr Nph Nba Nex Nsc Nor Dum Iwg Ilo Ias Res Ste Nre Cry Uni Cor Opt Aut + 1 7 1 0 2 1 0 1 0 0 1 0 0 0 0 0 0 0 1 +! +!Ipr Ppl Ioc Mat Pcr Ls1 Ls2 Ls3 NLI Prf Ins Rpa Sym Hkl Fou Sho Ana + 2 2 1 0 1 0 4 0 0 2 10 -1 0 0 0 0 1 +! +! Lambda1 Lambda2 Ratio Bkpos Wdt Cthm muR AsyLim Rpolarz 2nd-muR -> Patt# 1 + 1.622527 1.622527 0.00000 80.000 12.000 0.0000 0.7000 180.00 0.0000 0.0000 +! +!NCY Eps R_at R_an R_pr R_gl Thmin Step Thmax PSD Sent0 +200 0.10 0.04 0.04 0.04 0.04 4.1642 0.049998 163.7564 0.000 0.000 +! +! Excluded regions (LowT HighT) for Pattern# 1 + 0.00 10.00 + 164.00 180.00 +! +! Additional scattering factors for Pattern# 1 +B11 0.66500 0.00000 0 +! + 0 !Number of refined parameters +! +! Zero Code SyCos Code SySin Code Lambda Code MORE ->Patt# 1 + -0.21110 0.0 0.05281 0.0 0.09068 0.0 1.622527 0.00 0 +! Background coefficients/codes for Pattern# 1 (Polynomial of 6th degree) + 782.022 75.285 291.744 -3.149 -329.244 0.000 + 0.00 0.00 0.00 0.00 0.00 0.00 +!------------------------------------------------------------------------------- +! Data for PHASE number: 1 ==> Current R_Bragg for Pattern# 1: 3.5651 +!------------------------------------------------------------------------------- +nuclear +! +!Nat Dis Ang Pr1 Pr2 Pr3 Jbt Irf Isy Str Furth ATZ Nvk Npr More + 2 0 0 0.0 0.0 1.0 0 0 0 0 0 203.711 0 7 0 +! +! +P m -3 m <--Space group symbol +!Atom Typ X Y Z Biso Occ In Fin N_t Spc /Codes +La La 0.00000 0.00000 0.00000 0.59951 0.02083 0 0 0 0 + 0.00 0.00 0.00 0.00 0.00 +B B11 0.19978 0.50000 0.50000 0.44499 0.12500 0 0 0 0 + 0.00 0.00 0.00 0.00 0.00 +!-------> Profile Parameters for Pattern # 1 ----> Phase # 1 +! Scale Shape1 Bov Str1 Str2 Str3 Strain-Model + 141.1285 0.00000 0.00000 0.00000 0.00000 0.00000 0 + 0.00000 0.000 0.000 0.000 0.000 0.000 +! U V W X Y GauSiz LorSiz Size-Model + 0.089664 -0.375792 0.476524 0.000000 0.052425 0.000000 0.000000 0 + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 +! a b c alpha beta gamma # Cell Info + 4.156885 4.156885 4.156885 90.000000 90.000000 90.000000 + 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 +! Pref1 Pref2 Asy1 Asy2 Asy3 Asy4 S_L D_L + 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 +! 2Th1/TOF1 2Th2/TOF2 Pattern to plot + 10.000 163.756 1 diff --git a/docs/docs/verification/fullprof/pd-neut-cwl_tch-fcj_lab6/ECH0030684_LaB6_1p622A_noSLDL.prf b/docs/docs/verification/fullprof/pd-neut-cwl_tch-fcj_lab6/ECH0030684_LaB6_1p622A_noSLDL.prf new file mode 100644 index 000000000..b34c8ad37 --- /dev/null +++ b/docs/docs/verification/fullprof/pd-neut-cwl_tch-fcj_lab6/ECH0030684_LaB6_1p622A_noSLDL.prf @@ -0,0 +1,3266 @@ +IGOR +WAVES TwoTheta, Iobs, Icalc, Diff +BEGIN + 4.164 249.28 709.64 -460.36 + 4.214 242.77 710.04 -467.27 + 4.264 261.99 710.43 -448.44 + 4.314 374.47 710.83 -336.36 + 4.364 435.31 711.22 -275.91 + 4.414 647.92 711.61 -63.69 + 4.464 806.68 712.00 94.68 + 4.514 868.33 712.39 155.94 + 4.564 1082.78 712.78 370.00 + 4.614 1245.94 713.17 532.77 + 4.664 1161.56 713.55 448.01 + 4.714 1270.88 713.94 556.94 + 4.764 1353.10 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excl1 +BEGIN + 4.16 -1398 + 10.00 -1398 +END +WAVES Excrg2, excl2 +BEGIN + 164.00 -1398 + 163.76 -1398 +END +X Silent 1 +X DefaultFont Times +X Display Iobs, Icalc, Diff vs TwoTheta +X Modify mode(Iobs)=2, rgb(Iobs)=(0,0,0), rgb(Diff)=(3800,44400,4000) +X SetAxis bottom 4.16, 163.76 +X Modify lsize(Iobs)=2 +X Modify offset(Diff)={0, -13961} +X Modify wbRGB=(48483,64909,65535), gbRGB=(64612,65535,49415) +X Modify mirror(left)=2, mirror(bottom)=2 +X Modify gfSize=12 +X Append excl1 vs Excrg1 +X Modify mode(excl1)=7, hbFill(excl1)=4 +X Modify rgb(excl1)=(6421,62320,64794) +X Append excl2 vs Excrg2 +X Modify mode(excl2)=7, hbFill(excl2)=4 +X Modify rgb(excl2)=(6421,62320,64794) +X Append tik1 vs Phase1 +X Modify mode(tik1)=1 +X TextBox /F=2/S=3/A=RT "Files: ECH0030684_LaB6_1p622A_noSLDL\rDate of fit: \Z09 12/06/2026/ 14:15:21.5\Z12\rnuclear\rChi2 = 72.98" +X Label left "\Z14Intensity" +X Label bottom "\Z142-Theta (in degrees)" +X TileWindows/O=1/C +X ShowInfo +X | Title of data set: LaB6 Ge(331) +X | Date of run: 12/06/2026 / 14:15:21.5 +X Beep +X Beep diff --git a/docs/docs/verification/fullprof/pd-neut-cwl_tch-fcj_lab6/ECH0030684_LaB6_1p622A_noSLDL.sum b/docs/docs/verification/fullprof/pd-neut-cwl_tch-fcj_lab6/ECH0030684_LaB6_1p622A_noSLDL.sum new file mode 100644 index 000000000..05a973bae --- /dev/null +++ b/docs/docs/verification/fullprof/pd-neut-cwl_tch-fcj_lab6/ECH0030684_LaB6_1p622A_noSLDL.sum @@ -0,0 +1,143 @@ + + + ********************************************************** + ** PROGRAM FullProf.2k (Version 8.40 - Feb2026-ILL JRC) ** + ********************************************************** + M U L T I -- P A T T E R N + Rietveld, Profile Matching & Integrated Intensity + Refinement of X-ray and/or Neutron Data + + + Date: 12/06/2026 Time: 14:15:20.812 + + => PCR file code: ECH0030684_LaB6_1p622A_noSLDL + => DAT file code: ECH0030684_LaB6_1p62 -> Relative contribution: 1.0000 + => Title: LaB6 Ge(331) + + ==> CONDITIONS OF THIS RUN FOR PATTERN No.: 1 + + => Global Refinement of neutron powder data + => The 7th default profile function was selected + + => X-Y type of data: 2theta/TOF/E(Kev) Intens sigma for pattern: 1 + => Analysis of refinement at the end + => Wavelengths: 1.62253 1.62253 + => Cos(Monochromator angle)= 0.0000 + => Absorption correction (AC), muR-eff = 0.7000 0.0000 + => AC : Cylinder Debye-Scherrer (Hewat formula) + => Base of peaks: 2.0*HW* 12.00 + ==> Angular range, step and number of points: + 2Thmin: 4.164220 2Thmax: 163.756378 Step: 0.049998 No. of points: 3194 + =>-------> Pattern# 1 + => Crystal Structure Refinement for phase: 1 + => The density (volumic mass) of phase 1 is: 4.711 g/cm3 + => Scor: 4.0979 + + ==> RESULTS OF REFINEMENT: + + + => No. of fitted parameters: 0 + + +------------------------------------------------------------------------------ + => Phase No. 1 nuclear P m -3 m +------------------------------------------------------------------------------ + + => No. of reflections for pattern#: 1: 28 + + + ==> ATOM PARAMETERS: + + Name x sx y sy z sz B sB occ. socc. Mult + La 0.00000( 0) 0.00000( 0) 0.00000( 0) 0.600( 0) 0.021( 0) 1 + B 0.19978( 0) 0.50000( 0) 0.50000( 0) 0.445( 0) 0.125( 0) 6 + + ==> PROFILE PARAMETERS FOR PATTERN# 1 + + => Cell parameters : + 4.15689 0.00000 + 4.15689 0.00000 + 4.15689 0.00000 + 90.00000 0.00000 + 90.00000 0.00000 + 90.00000 0.00000 + + => overall scale factor : 141.1285 0.000000 + => Eta(p-v) or m(p-vii) : 0.00000 0.00000 + => Overall tem. factor : 0.00000 0.00000 + => Halfwidth parameters : 0.08966 0.00000 + -0.37579 0.00000 + 0.47652 0.00000 + => Preferred orientation: 0.00000 0.00000 + 0.00000 0.00000 + => Asymmetry parameters : 0.00000 0.00000 + 0.00000 0.00000 + 0.00000 0.00000 + 0.00000 0.00000 + => X and y parameters : 0.00000 0.00000 + 0.05243 0.00000 + => Strain parameters : 0.00000 0.00000 + 0.00000 0.00000 + 0.00000 0.00000 + => Size parameters (G,L): 0.00000 0.00000 + 0.00000 0.00000 + + => Add. shape parameters: + 0.00000 0.00000 + 0.00000 0.00000 + + + + ==> GLOBAL PARAMETERS FOR PATTERN# 1 + + + => Zero-point: -0.2111 0.0000 + => Background Polynomial Parameters ==> + 782.02 0.0000 + 75.285 0.0000 + 291.74 0.0000 + -3.1490 0.0000 + -329.24 0.0000 + 0.0000 0.0000 + + => Cos(2theta)-shift parameter : 0.0528 0.0000 + => Sin(2theta)-shift parameter : 0.0907 0.0000 + + ==> RELIABILITY FACTORS WITH ALL NON-EXCLUDED POINTS FOR PATTERN: 1 + + => Cycle: 1 => MaxCycle:200 + => N-P+C: 3076 + => R-factors (not corrected for background) for Pattern: 1 + => Rp: 16.7 Rwp: 23.6 Rexp: 2.76 Chi2: 73.0 L.S. refinement + => Conventional Rietveld R-factors for Pattern: 1 + => Rp: 33.1 Rwp: 40.1 Rexp: 4.69 Chi2: 73.0 + => Deviance: 0.335E+06 Dev* : 108.8 + => DW-Stat.: 0.0683 DW-exp: 1.8880 + => N-sigma of the GoF: 2823.015 + + ==> RELIABILITY FACTORS FOR POINTS WITH BRAGG CONTRIBUTIONS FOR PATTERN: 1 + + => N-P+C: 2989 + => R-factors (not corrected for background) for Pattern: 1 + => Rp: 16.8 Rwp: 23.7 Rexp: 2.74 Chi2: 75.1 L.S. refinement + => Conventional Rietveld R-factors for Pattern: 1 + => Rp: 33.0 Rwp: 40.1 Rexp: 4.62 Chi2: 75.1 + => Deviance: 0.335E+06 Dev* : 111.9 + => DW-Stat.: 0.0683 DW-exp: 1.8863 + => N-sigma of the GoF: 2863.702 + + => Global user-weigthed Chi2 (Bragg contrib.): 75.1 + + ----------------------------------------------------- + BRAGG R-Factors and weight fractions for Pattern # 1 + ----------------------------------------------------- + + => Phase: 1 nuclear + => Bragg R-factor: 3.57 Vol: 71.830( 0.000) Fract(%): 100.00( 0.00) + => Rf-factor= 2.15 ATZ: 203.711 Brindley: 1.0000 + + + CPU Time: 0.859 seconds + 0.014 minutes + + => Run finished at: Date: 12/06/2026 Time: 14:15:21.675 diff --git a/docs/docs/verification/index.md b/docs/docs/verification/index.md index 1a172d7f2..121fa11ac 100644 --- a/docs/docs/verification/index.md +++ b/docs/docs/verification/index.md @@ -58,8 +58,13 @@ and so on. The list below notes only what is specific to each page. asymmetry is crysfml-only. - [LaB₆ `pd-neut-cwl` (absorption)](pd-neut-cwl_tch-fcj_lab6.ipynb) – Lanthanum hexaboride (LaB₆, _Pm-3m_); adds Debye–Scherrer sample - absorption (μR) on top of FCJ asymmetry. Skipped in CI: sample - absorption is modelled by neither engine. + absorption (μR = 0.7), now modelled by both engines, on top of FCJ + asymmetry. Skipped in CI: FCJ asymmetry is crysfml-only. +- [LaB₆ `pd-neut-cwl` (absorption, no FCJ)](pd-neut-cwl_tch-fcj-nosldl_lab6.ipynb) + – Lanthanum hexaboride (LaB₆, _Pm-3m_); Debye–Scherrer sample + absorption (μR = 0.7) with FCJ asymmetry switched off, isolating the + absorption correction. ed-cryspy matches FullProf (enabling the + correction removes a ≈ 2.9× intensity mismatch). ## Powder, neutron, time-of-flight diff --git a/docs/docs/verification/pd-neut-cwl_tch-fcj-nosldl_lab6.ipynb b/docs/docs/verification/pd-neut-cwl_tch-fcj-nosldl_lab6.ipynb new file mode 100644 index 000000000..142be0afa --- /dev/null +++ b/docs/docs/verification/pd-neut-cwl_tch-fcj-nosldl_lab6.ipynb @@ -0,0 +1,309 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": null, + "id": "0", + "metadata": { + "tags": [ + "hide-in-docs" + ] + }, + "outputs": [], + "source": [ + "# Check whether easydiffraction is installed; install it if needed.\n", + "# Required for remote environments such as Google Colab.\n", + "import importlib.util\n", + "\n", + "if importlib.util.find_spec('easydiffraction') is None:\n", + " %pip install easydiffraction" + ] + }, + { + "cell_type": "markdown", + "id": "1", + "metadata": {}, + "source": [ + "# LaB₆ — neutron powder, constant wavelength, sample absorption (no FCJ)" + ] + }, + { + "cell_type": "markdown", + "id": "2", + "metadata": {}, + "source": [ + "This page isolates the new Debye–Scherrer **sample-absorption**\n", + "correction. The FullProf reference uses μR = 0.7 with the\n", + "Finger–Cox–Jephcoat axial-divergence asymmetry switched off\n", + "(S_L = D_L = 0), so the absorption correction is the only remaining\n", + "angle-dependent intensity effect.\n", + "\n", + "The agreement is asserted against **ed-cryspy**, whose base intensities\n", + "match FullProf for this sample. Without the correction the calculated\n", + "pattern is ≈ 2.9× too intense (the FullProf reference is attenuated by\n", + "absorption); enabling `cylinder-hewat` with μR = 0.7 brings ed-cryspy\n", + "into agreement with FullProf. ed-crysfml is shown for completeness but\n", + "not asserted: it has a separate, pre-existing intensity-convention\n", + "difference with FullProf for LaB₆ that is independent of absorption." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "3", + "metadata": {}, + "outputs": [], + "source": [ + "import easydiffraction as ed\n", + "from easydiffraction import ExperimentFactory\n", + "from easydiffraction import StructureFactory\n", + "from easydiffraction.analysis import verification as verify" + ] + }, + { + "cell_type": "markdown", + "id": "4", + "metadata": {}, + "source": [ + "## Build the project" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "5", + "metadata": {}, + "outputs": [], + "source": [ + "project = ed.Project()" + ] + }, + { + "cell_type": "markdown", + "id": "6", + "metadata": {}, + "source": [ + "## Define the structure" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "7", + "metadata": {}, + "outputs": [], + "source": [ + "structure = StructureFactory.from_scratch(name='lab6')\n", + "structure.space_group.name_h_m = 'P m -3 m' # FullProf Space group symbol\n", + "structure.cell.length_a = 4.156885 # FullProf a\n", + "structure.atom_sites.create(\n", + " label='La', # FullProf Atom\n", + " type_symbol='La', # FullProf Typ\n", + " fract_x=0.0, # FullProf X\n", + " fract_y=0.0, # FullProf Y\n", + " fract_z=0.0, # FullProf Z\n", + " adp_type='Biso', # FullProf Biso\n", + " adp_iso=0.59951, # FullProf Biso\n", + ")\n", + "structure.atom_sites.create(\n", + " label='B', # FullProf Atom\n", + " type_symbol='11B', # FullProf \"B11\"\n", + " fract_x=0.19978, # FullProf X\n", + " fract_y=0.5, # FullProf Y\n", + " fract_z=0.5, # FullProf Z\n", + " adp_type='Biso', # FullProf Biso\n", + " adp_iso=0.44499, # FullProf Biso\n", + ")\n", + "\n", + "project.structures.add(structure)" + ] + }, + { + "cell_type": "markdown", + "id": "8", + "metadata": {}, + "source": [ + "## Load the FullProf reference" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "9", + "metadata": {}, + "outputs": [], + "source": [ + "FULLPROF_PROJECT_DIR = 'pd-neut-cwl_tch-fcj_lab6'\n", + "FULLPROF_PRF_FILE = 'ECH0030684_LaB6_1p622A_noSLDL.prf'\n", + "FULLPROF_BAC_FILE = 'ECH0030684_LaB6_1p622A_noSLDL.bac'\n", + "FULLPROF_ZERO = -0.21110 # FullProf Zero\n", + "FULLPROF_SCALE = 141.1285 # FullProf Scale\n", + "FULLPROF_WAVELENGTH = 1.622527 # FullProf Lambda\n", + "FULLPROF_U = 0.089664 # FullProf U\n", + "FULLPROF_V = -0.375792 # FullProf V\n", + "FULLPROF_W = 0.476524 # FullProf W\n", + "FULLPROF_X = 0.0 # FullProf X\n", + "FULLPROF_Y = 0.052425 # FullProf Y\n", + "FULLPROF_SYCOS = 0.05281 # FullProf SyCos\n", + "FULLPROF_SYSIN = 0.09068 # FullProf SySin\n", + "FULLPROF_MU_R = 0.7 # FullProf muR (cylindrical absorption)\n", + "\n", + "x, calc_fullprof = verify.load_fullprof_calc_profile(\n", + " FULLPROF_PROJECT_DIR,\n", + " FULLPROF_PRF_FILE,\n", + " FULLPROF_BAC_FILE,\n", + " FULLPROF_ZERO,\n", + ")" + ] + }, + { + "cell_type": "markdown", + "id": "10", + "metadata": {}, + "source": [ + "## Create the experiment" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "11", + "metadata": {}, + "outputs": [], + "source": [ + "experiment = ExperimentFactory.from_scratch(\n", + " name='lab6',\n", + " sample_form='powder',\n", + " beam_mode='constant wavelength',\n", + " radiation_probe='neutron',\n", + " scattering_type='bragg',\n", + ")\n", + "verify.set_reference_as_measured(experiment, x, calc_fullprof)\n", + "\n", + "experiment.linked_phases.create(id='lab6', scale=FULLPROF_SCALE)\n", + "\n", + "experiment.instrument.setup_wavelength = FULLPROF_WAVELENGTH\n", + "experiment.instrument.calib_twotheta_offset = FULLPROF_ZERO\n", + "\n", + "experiment.peak.broad_gauss_u = FULLPROF_U\n", + "experiment.peak.broad_gauss_v = FULLPROF_V\n", + "experiment.peak.broad_gauss_w = FULLPROF_W\n", + "experiment.peak.broad_lorentz_x = FULLPROF_X\n", + "experiment.peak.broad_lorentz_y = FULLPROF_Y\n", + "\n", + "# Sample absorption (Debye-Scherrer cylinder, muR = 0.7) is modelled by\n", + "# both engines via the calculator-independent A(theta) envelope. No FCJ\n", + "# asymmetry is applied (the reference has S_L = D_L = 0).\n", + "experiment.absorption.type = 'cylinder-hewat'\n", + "experiment.absorption.mu_r = FULLPROF_MU_R\n", + "\n", + "project.experiments.add(experiment)" + ] + }, + { + "cell_type": "markdown", + "id": "12", + "metadata": {}, + "source": [ + "## ed-cryspy VS FullProf" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "13", + "metadata": {}, + "outputs": [], + "source": [ + "experiment.calculator.type = 'cryspy'\n", + "\n", + "experiment.instrument.calib_sample_displacement = FULLPROF_SYCOS\n", + "experiment.instrument.calib_sample_transparency = FULLPROF_SYSIN\n", + "\n", + "project.analysis.calculate()\n", + "calc_ed_cryspy = experiment.data.intensity_calc\n", + "\n", + "project.display.pattern_comparison(\n", + " 'lab6',\n", + " reference=calc_fullprof,\n", + " candidate=calc_ed_cryspy,\n", + " reference_label='FullProf',\n", + " candidate_label='ed-cryspy',\n", + ")" + ] + }, + { + "cell_type": "markdown", + "id": "14", + "metadata": {}, + "source": [ + "## ed-crysfml VS FullProf" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "15", + "metadata": {}, + "outputs": [], + "source": [ + "experiment.calculator.type = 'crysfml'\n", + "\n", + "experiment.peak.type = 'thompson-cox-hastings'\n", + "experiment.instrument.calib_twotheta_offset = FULLPROF_ZERO\n", + "experiment.peak.broad_gauss_u = FULLPROF_U\n", + "experiment.peak.broad_gauss_v = FULLPROF_V\n", + "experiment.peak.broad_gauss_w = FULLPROF_W\n", + "experiment.peak.broad_lorentz_x = FULLPROF_X\n", + "experiment.peak.broad_lorentz_y = FULLPROF_Y\n", + "\n", + "project.analysis.calculate()\n", + "calc_ed_crysfml = experiment.data.intensity_calc\n", + "\n", + "project.display.pattern_comparison(\n", + " 'lab6',\n", + " reference=calc_fullprof,\n", + " candidate=calc_ed_crysfml,\n", + " reference_label='FullProf',\n", + " candidate_label='ed-crysfml',\n", + ")" + ] + }, + { + "cell_type": "markdown", + "id": "16", + "metadata": {}, + "source": [ + "## Agreement check\n", + "\n", + "Only ed-cryspy is asserted (see the note at the top): enabling the\n", + "`cylinder-hewat` absorption brings it into agreement with the\n", + "absorption-corrected FullProf reference." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "17", + "metadata": {}, + "outputs": [], + "source": [ + "verify.assert_patterns_agree(\n", + " [\n", + " ('cryspy vs FullProf', calc_fullprof, calc_ed_cryspy),\n", + " ],\n", + " raise_on_failure=True,\n", + ")" + ] + } + ], + "metadata": { + "jupytext": { + "cell_metadata_filter": "-all", + "main_language": "python", + "notebook_metadata_filter": "-all" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/docs/docs/verification/pd-neut-cwl_tch-fcj-nosldl_lab6.py b/docs/docs/verification/pd-neut-cwl_tch-fcj-nosldl_lab6.py new file mode 100644 index 000000000..cff6b852b --- /dev/null +++ b/docs/docs/verification/pd-neut-cwl_tch-fcj-nosldl_lab6.py @@ -0,0 +1,175 @@ +# %% [markdown] +# # LaB₆ — neutron powder, constant wavelength, sample absorption (no FCJ) + +# %% [markdown] +# This page isolates the new Debye–Scherrer **sample-absorption** +# correction. The FullProf reference uses μR = 0.7 with the +# Finger–Cox–Jephcoat axial-divergence asymmetry switched off +# (S_L = D_L = 0), so the absorption correction is the only remaining +# angle-dependent intensity effect. +# +# The agreement is asserted against **ed-cryspy**, whose base intensities +# match FullProf for this sample. Without the correction the calculated +# pattern is ≈ 2.9× too intense (the FullProf reference is attenuated by +# absorption); enabling `cylinder-hewat` with μR = 0.7 brings ed-cryspy +# into agreement with FullProf. ed-crysfml is shown for completeness but +# not asserted: it has a separate, pre-existing intensity-convention +# difference with FullProf for LaB₆ that is independent of absorption. + +# %% +import easydiffraction as ed +from easydiffraction import ExperimentFactory +from easydiffraction import StructureFactory +from easydiffraction.analysis import verification as verify + +# %% [markdown] +# ## Build the project + +# %% +project = ed.Project() + +# %% [markdown] +# ## Define the structure + +# %% +structure = StructureFactory.from_scratch(name='lab6') +structure.space_group.name_h_m = 'P m -3 m' # FullProf Space group symbol +structure.cell.length_a = 4.156885 # FullProf a +structure.atom_sites.create( + label='La', # FullProf Atom + type_symbol='La', # FullProf Typ + fract_x=0.0, # FullProf X + fract_y=0.0, # FullProf Y + fract_z=0.0, # FullProf Z + adp_type='Biso', # FullProf Biso + adp_iso=0.59951, # FullProf Biso +) +structure.atom_sites.create( + label='B', # FullProf Atom + type_symbol='11B', # FullProf "B11" + fract_x=0.19978, # FullProf X + fract_y=0.5, # FullProf Y + fract_z=0.5, # FullProf Z + adp_type='Biso', # FullProf Biso + adp_iso=0.44499, # FullProf Biso +) + +project.structures.add(structure) + +# %% [markdown] +# ## Load the FullProf reference + +# %% +FULLPROF_PROJECT_DIR = 'pd-neut-cwl_tch-fcj_lab6' +FULLPROF_PRF_FILE = 'ECH0030684_LaB6_1p622A_noSLDL.prf' +FULLPROF_BAC_FILE = 'ECH0030684_LaB6_1p622A_noSLDL.bac' +FULLPROF_ZERO = -0.21110 # FullProf Zero +FULLPROF_SCALE = 141.1285 # FullProf Scale +FULLPROF_WAVELENGTH = 1.622527 # FullProf Lambda +FULLPROF_U = 0.089664 # FullProf U +FULLPROF_V = -0.375792 # FullProf V +FULLPROF_W = 0.476524 # FullProf W +FULLPROF_X = 0.0 # FullProf X +FULLPROF_Y = 0.052425 # FullProf Y +FULLPROF_SYCOS = 0.05281 # FullProf SyCos +FULLPROF_SYSIN = 0.09068 # FullProf SySin +FULLPROF_MU_R = 0.7 # FullProf muR (cylindrical absorption) + +x, calc_fullprof = verify.load_fullprof_calc_profile( + FULLPROF_PROJECT_DIR, + FULLPROF_PRF_FILE, + FULLPROF_BAC_FILE, + FULLPROF_ZERO, +) + +# %% [markdown] +# ## Create the experiment + +# %% +experiment = ExperimentFactory.from_scratch( + name='lab6', + sample_form='powder', + beam_mode='constant wavelength', + radiation_probe='neutron', + scattering_type='bragg', +) +verify.set_reference_as_measured(experiment, x, calc_fullprof) + +experiment.linked_phases.create(id='lab6', scale=FULLPROF_SCALE) + +experiment.instrument.setup_wavelength = FULLPROF_WAVELENGTH +experiment.instrument.calib_twotheta_offset = FULLPROF_ZERO + +experiment.peak.broad_gauss_u = FULLPROF_U +experiment.peak.broad_gauss_v = FULLPROF_V +experiment.peak.broad_gauss_w = FULLPROF_W +experiment.peak.broad_lorentz_x = FULLPROF_X +experiment.peak.broad_lorentz_y = FULLPROF_Y + +# Sample absorption (Debye-Scherrer cylinder, muR = 0.7) is modelled by +# both engines via the calculator-independent A(theta) envelope. No FCJ +# asymmetry is applied (the reference has S_L = D_L = 0). +experiment.absorption.type = 'cylinder-hewat' +experiment.absorption.mu_r = FULLPROF_MU_R + +project.experiments.add(experiment) + +# %% [markdown] +# ## ed-cryspy VS FullProf + +# %% +experiment.calculator.type = 'cryspy' + +experiment.instrument.calib_sample_displacement = FULLPROF_SYCOS +experiment.instrument.calib_sample_transparency = FULLPROF_SYSIN + +project.analysis.calculate() +calc_ed_cryspy = experiment.data.intensity_calc + +project.display.pattern_comparison( + 'lab6', + reference=calc_fullprof, + candidate=calc_ed_cryspy, + reference_label='FullProf', + candidate_label='ed-cryspy', +) + +# %% [markdown] +# ## ed-crysfml VS FullProf + +# %% +experiment.calculator.type = 'crysfml' + +experiment.peak.type = 'thompson-cox-hastings' +experiment.instrument.calib_twotheta_offset = FULLPROF_ZERO +experiment.peak.broad_gauss_u = FULLPROF_U +experiment.peak.broad_gauss_v = FULLPROF_V +experiment.peak.broad_gauss_w = FULLPROF_W +experiment.peak.broad_lorentz_x = FULLPROF_X +experiment.peak.broad_lorentz_y = FULLPROF_Y + +project.analysis.calculate() +calc_ed_crysfml = experiment.data.intensity_calc + +project.display.pattern_comparison( + 'lab6', + reference=calc_fullprof, + candidate=calc_ed_crysfml, + reference_label='FullProf', + candidate_label='ed-crysfml', +) + +# %% [markdown] +# ## Agreement check +# +# Only ed-cryspy is asserted (see the note at the top): enabling the +# `cylinder-hewat` absorption brings it into agreement with the +# absorption-corrected FullProf reference. + +# %% +verify.assert_patterns_agree( + [ + ('cryspy vs FullProf', calc_fullprof, calc_ed_cryspy), + ], + raise_on_failure=True, +) diff --git a/docs/docs/verification/pd-neut-cwl_tch-fcj_lab6.ipynb b/docs/docs/verification/pd-neut-cwl_tch-fcj_lab6.ipynb index e16a57cc2..6d833be3d 100644 --- a/docs/docs/verification/pd-neut-cwl_tch-fcj_lab6.ipynb +++ b/docs/docs/verification/pd-neut-cwl_tch-fcj_lab6.ipynb @@ -128,6 +128,7 @@ "FULLPROF_SYSIN = 0.09068 # FullProf SySin\n", "FULLPROF_S_L = 0.08000 # FullProf S_L\n", "FULLPROF_D_L = 0.08000 # FullProf D_L\n", + "FULLPROF_MU_R = 0.7 # FullProf muR (cylindrical absorption)\n", "\n", "x, calc_fullprof = verify.load_fullprof_calc_profile(\n", " FULLPROF_PROJECT_DIR,\n", @@ -173,7 +174,12 @@ "experiment.peak.broad_lorentz_y = FULLPROF_Y\n", "# Engine-specific corrections are applied in each engine's section below:\n", "# SyCos/SySin (cryspy only) and the FCJ S_L/D_L asymmetry (crysfml only).\n", - "# Sample absorption (muR = 0.7) is modelled by neither engine.\n", + "\n", + "# Sample absorption (Debye-Scherrer cylinder, muR = 0.7) is modelled by\n", + "# both engines via the calculator-independent A(theta) envelope, so it is\n", + "# set once here and applies to every calculation below.\n", + "experiment.absorption.type = 'cylinder-hewat'\n", + "experiment.absorption.mu_r = FULLPROF_MU_R\n", "\n", "project.experiments.add(experiment)" ] diff --git a/docs/docs/verification/pd-neut-cwl_tch-fcj_lab6.py b/docs/docs/verification/pd-neut-cwl_tch-fcj_lab6.py index 0a56a92e8..439ffed0c 100644 --- a/docs/docs/verification/pd-neut-cwl_tch-fcj_lab6.py +++ b/docs/docs/verification/pd-neut-cwl_tch-fcj_lab6.py @@ -60,6 +60,7 @@ FULLPROF_SYSIN = 0.09068 # FullProf SySin FULLPROF_S_L = 0.08000 # FullProf S_L FULLPROF_D_L = 0.08000 # FullProf D_L +FULLPROF_MU_R = 0.7 # FullProf muR (cylindrical absorption) x, calc_fullprof = verify.load_fullprof_calc_profile( FULLPROF_PROJECT_DIR, @@ -93,7 +94,12 @@ experiment.peak.broad_lorentz_y = FULLPROF_Y # Engine-specific corrections are applied in each engine's section below: # SyCos/SySin (cryspy only) and the FCJ S_L/D_L asymmetry (crysfml only). -# Sample absorption (muR = 0.7) is modelled by neither engine. + +# Sample absorption (Debye-Scherrer cylinder, muR = 0.7) is modelled by +# both engines via the calculator-independent A(theta) envelope, so it is +# set once here and applies to every calculation below. +experiment.absorption.type = 'cylinder-hewat' +experiment.absorption.mu_r = FULLPROF_MU_R project.experiments.add(experiment) diff --git a/docs/mkdocs.yml b/docs/mkdocs.yml index f4e08d6f4..f95e4458c 100644 --- a/docs/mkdocs.yml +++ b/docs/mkdocs.yml @@ -263,6 +263,7 @@ nav: - LaB6 (SyCos/SySin): verification/pd-neut-cwl_tch-fcj-noabs-nosldl_lab6.ipynb - LaB6 (FCJ asymmetry): verification/pd-neut-cwl_tch-fcj-noabs_lab6.ipynb - LaB6 (absorption): verification/pd-neut-cwl_tch-fcj_lab6.ipynb + - LaB6 (absorption, no FCJ): verification/pd-neut-cwl_tch-fcj-nosldl_lab6.ipynb - Powder, neutron, time-of-flight: - Si (Jorgensen): verification/pd-neut-tof_j_si.ipynb - Si (Jorgensen–Von Dreele): verification/pd-neut-tof_jvd_si.ipynb diff --git a/src/easydiffraction/analysis/calculators/absorption.py b/src/easydiffraction/analysis/calculators/absorption.py new file mode 100644 index 000000000..1edeca580 --- /dev/null +++ b/src/easydiffraction/analysis/calculators/absorption.py @@ -0,0 +1,116 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause +""" +Calculator-independent sample-absorption correction factor. + +The correction is a slowly varying envelope of ``sin^2(theta)``, so it +is applied pointwise to the calculated pattern by both backends rather +than per reflection. This keeps the cryspy and crysfml results +bit-for-bit consistent on the absorption term. +""" + +from __future__ import annotations + +import numpy as np + +from easydiffraction.datablocks.experiment.item.enums import AbsorptionTypeEnum +from easydiffraction.utils.logging import log + +# Upper muR for which the Hewat cylindrical expansion is validated to +# four decimals against FullProf. Beyond this a Lobanov form is +# preferable; the current code extrapolates and warns rather than fails. +HEWAT_MAX_VALIDATED_MU_R = 1.5 + +# muR values already warned about, so the out-of-range warning fires +# once per distinct value rather than on every pattern evaluation during +# a refinement. +_WARNED_MU_R: set[float] = set() + + +def apply(y: object, experiment: object) -> object: + """ + Apply the sample-absorption correction to a calculated pattern. + + Shared by both backends so the absorption term stays identical + across calculators. The pattern is returned unchanged when the + experiment exposes no ``absorption`` category (single-crystal / + total scattering), or when it is empty or its length does not match + the 2-theta grid (the backends' "no calculated data" paths). + + Parameters + ---------- + y : object + Calculated intensities (NumPy array or list). + experiment : object + Experiment providing ``data.x`` (the 2-theta grid) and, when + applicable, the active ``absorption`` category. + + Returns + ------- + object + Corrected intensities, or ``y`` unchanged when no correction + applies. + """ + if not hasattr(experiment, 'absorption'): + return y + y_values = np.asarray(y, dtype=float) + two_theta = np.asarray(experiment.data.x, dtype=float) + if y_values.size == 0 or y_values.shape != two_theta.shape: + return y + return y_values * factor(two_theta, experiment.absorption) + + +def factor(two_theta: np.ndarray, absorption: object) -> np.ndarray: + """ + Return the per-point sample-absorption correction A. + + Parameters + ---------- + two_theta : np.ndarray + Scattering angle 2-theta grid in degrees. + absorption : object + Active absorption category (its ``type_info.tag`` selects the + correction form). + + Returns + ------- + np.ndarray + Multiplicative correction A with the same shape as + ``two_theta``; all ones when no correction applies. + """ + two_theta = np.asarray(two_theta, dtype=float) + tag = absorption.type_info.tag + if tag == AbsorptionTypeEnum.CYLINDER_HEWAT.value: + return _hewat_cylinder(two_theta, absorption.mu_r.value) + return np.ones_like(two_theta) + + +def _hewat_cylinder(two_theta: np.ndarray, mu_r: float) -> np.ndarray: + """ + Return the Hewat cylindrical Debye-Scherrer absorption factor. + + Parameters + ---------- + two_theta : np.ndarray + Scattering angle 2-theta grid in degrees. + mu_r : float + Linear absorption coefficient times sample radius (muR). + + Returns + ------- + np.ndarray + ``A = exp(-(1.7133 - 0.0368 sin^2 t) muR + + (0.0927 + 0.375 sin^2 t) muR^2)``. + """ + if mu_r > HEWAT_MAX_VALIDATED_MU_R: + rounded = round(mu_r, 4) + if rounded not in _WARNED_MU_R: + _WARNED_MU_R.add(rounded) + log.warning( + f'Absorption muR={mu_r:g} exceeds the Hewat-validated ' + f'range (<= {HEWAT_MAX_VALIDATED_MU_R}); the result is ' + 'extrapolated. A Lobanov form is preferable for large muR.' + ) + theta = np.radians(two_theta) / 2.0 + sin2 = np.sin(theta) ** 2 + return np.exp(-(1.7133 - 0.0368 * sin2) * mu_r + (0.0927 + 0.375 * sin2) * mu_r**2) diff --git a/src/easydiffraction/analysis/calculators/crysfml.py b/src/easydiffraction/analysis/calculators/crysfml.py index 37d64ffb5..863616dc8 100644 --- a/src/easydiffraction/analysis/calculators/crysfml.py +++ b/src/easydiffraction/analysis/calculators/crysfml.py @@ -10,6 +10,7 @@ import numpy as np +from easydiffraction.analysis.calculators import absorption as absorption_correction from easydiffraction.analysis.calculators.base import CalculatorBase from easydiffraction.analysis.calculators.factory import CalculatorFactory from easydiffraction.core.metadata import TypeInfo @@ -166,7 +167,7 @@ def calculate_pattern( except KeyError: log.warning('[CrysfmlCalculator] No calculated data') y = [] - return np.asarray(y) + return np.asarray(absorption_correction.apply(y, experiment)) def _calculate_adjusted_pattern( self, diff --git a/src/easydiffraction/analysis/calculators/cryspy.py b/src/easydiffraction/analysis/calculators/cryspy.py index eb36ac1eb..9e92de1d9 100644 --- a/src/easydiffraction/analysis/calculators/cryspy.py +++ b/src/easydiffraction/analysis/calculators/cryspy.py @@ -12,6 +12,7 @@ import numpy as np +from easydiffraction.analysis.calculators import absorption as absorption_correction from easydiffraction.analysis.calculators.base import CalculatorBase from easydiffraction.analysis.calculators.base import PowderReflnRecord from easydiffraction.analysis.calculators.factory import CalculatorFactory @@ -300,7 +301,7 @@ def calculate_pattern( log.warning(f'[CryspyCalculator] No calculated data for {cryspy_block_name}') return [] - return y_calc + return absorption_correction.apply(y_calc, experiment) def last_powder_refln_records( self, diff --git a/src/easydiffraction/datablocks/experiment/categories/absorption/__init__.py b/src/easydiffraction/datablocks/experiment/categories/absorption/__init__.py new file mode 100644 index 000000000..b310480dc --- /dev/null +++ b/src/easydiffraction/datablocks/experiment/categories/absorption/__init__.py @@ -0,0 +1,10 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause +""" +Sample-absorption correction category (cylindrical Debye-Scherrer). +""" + +from easydiffraction.datablocks.experiment.categories.absorption.cylinder_hewat import ( + CylinderHewatAbsorption, +) +from easydiffraction.datablocks.experiment.categories.absorption.none import NoAbsorption diff --git a/src/easydiffraction/datablocks/experiment/categories/absorption/base.py b/src/easydiffraction/datablocks/experiment/categories/absorption/base.py new file mode 100644 index 000000000..8617bfbac --- /dev/null +++ b/src/easydiffraction/datablocks/experiment/categories/absorption/base.py @@ -0,0 +1,83 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause +"""Base class for sample-absorption correction categories.""" + +from __future__ import annotations + +from easydiffraction.core.category import CategoryItem +from easydiffraction.core.switchable import SwitchableCategoryBase +from easydiffraction.core.validation import AttributeSpec +from easydiffraction.core.validation import MembershipValidator +from easydiffraction.core.variable import StringDescriptor +from easydiffraction.datablocks.experiment.categories.absorption.factory import AbsorptionFactory +from easydiffraction.datablocks.experiment.item.enums import AbsorptionTypeEnum +from easydiffraction.io.cif.handler import CifHandler + + +class AbsorptionBase(CategoryItem, SwitchableCategoryBase): + """Base class for sample-absorption correction categories.""" + + _category_code = 'absorption' + _owner_attr_name = 'absorption' + _swap_method_name = '_swap_absorption' + + def __init__(self) -> None: + super().__init__() + + type_info = getattr(type(self), 'type_info', None) + default_tag = type_info.tag if type_info is not None else '' + self._type: StringDescriptor = StringDescriptor( + name='type', + description='Active absorption type tag', + value_spec=AttributeSpec( + default=default_tag, + validator=MembershipValidator( + allowed=[member.value for member in AbsorptionTypeEnum], + ), + ), + cif_handler=CifHandler( + names=['_absorption.type'], + iucr_name='_easydiffraction_absorption.type', + ), + ) + + @staticmethod + def _supported_types( + filters: dict[str, object], + ) -> list[tuple[str, str]]: + """Return absorption types supported for owner filters.""" + return [ + (klass.type_info.tag, klass.type_info.description) + for klass in AbsorptionFactory.supported_for( + calculator=filters.get('calculator'), + sample_form=filters.get('sample_form'), + scattering_type=filters.get('scattering_type'), + beam_mode=filters.get('beam_mode'), + radiation_probe=filters.get('radiation_probe'), + ) + ] + + def from_cif(self, block: object, idx: int = 0) -> None: + """ + Populate parameters from CIF, skipping the active-type selector. + + ``_absorption.type`` is restored with owner-context validation + by ``_restore_switchable_types`` before parameters are loaded. + Re-loading it through the generic descriptor path would set the + public ``type`` selector even when the persisted tag was + rejected for the experiment context (for example a CWL-only + ``cylinder-hewat`` tag in a time-of-flight file), leaving the + live category and its selector inconsistent. The type descriptor + is therefore intentionally skipped here. + + Parameters + ---------- + block : object + Parsed CIF block to read parameter values from. + idx : int, default=0 + Loop index for the parameter values. + """ + for param in self.parameters: + if param is self._type: + continue + param.from_cif(block, idx=idx) diff --git a/src/easydiffraction/datablocks/experiment/categories/absorption/cylinder_hewat.py b/src/easydiffraction/datablocks/experiment/categories/absorption/cylinder_hewat.py new file mode 100644 index 000000000..f65ea342b --- /dev/null +++ b/src/easydiffraction/datablocks/experiment/categories/absorption/cylinder_hewat.py @@ -0,0 +1,89 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause +"""Cylindrical Debye-Scherrer absorption correction (Hewat).""" + +from __future__ import annotations + +from easydiffraction.core.display_handler import DisplayHandler +from easydiffraction.core.metadata import CalculatorSupport +from easydiffraction.core.metadata import Compatibility +from easydiffraction.core.metadata import TypeInfo +from easydiffraction.core.validation import AttributeSpec +from easydiffraction.core.validation import RangeValidator +from easydiffraction.core.variable import Parameter +from easydiffraction.datablocks.experiment.categories.absorption.base import AbsorptionBase +from easydiffraction.datablocks.experiment.categories.absorption.factory import AbsorptionFactory +from easydiffraction.datablocks.experiment.item.enums import AbsorptionTypeEnum +from easydiffraction.datablocks.experiment.item.enums import BeamModeEnum +from easydiffraction.datablocks.experiment.item.enums import CalculatorEnum +from easydiffraction.datablocks.experiment.item.enums import SampleFormEnum +from easydiffraction.datablocks.experiment.item.enums import ScatteringTypeEnum +from easydiffraction.io.cif.handler import CifHandler + + +@AbsorptionFactory.register +class CylinderHewatAbsorption(AbsorptionBase): + """ + Cylindrical Debye-Scherrer absorption correction (Hewat). + + Applies the angle-dependent transmission factor + + ``A(θ) = exp(-(1.7133 - 0.0368·sin²θ)·μR + + (0.0927 + 0.375·sin²θ)·μR²)`` + + for a cylindrical sample, where ``μR`` is the linear absorption + coefficient times the sample radius. Validated to four decimals + against FullProf for μR ≲ 1.5; for larger μR a Lobanov form is + preferable (not yet implemented). + """ + + type_info = TypeInfo( + tag=AbsorptionTypeEnum.CYLINDER_HEWAT.value, + description=AbsorptionTypeEnum.CYLINDER_HEWAT.description(), + ) + compatibility = Compatibility( + sample_form=frozenset({SampleFormEnum.POWDER}), + scattering_type=frozenset({ScatteringTypeEnum.BRAGG}), + beam_mode=frozenset({BeamModeEnum.CONSTANT_WAVELENGTH}), + ) + calculator_support = CalculatorSupport( + calculators=frozenset({CalculatorEnum.CRYSPY, CalculatorEnum.CRYSFML}), + ) + + def __init__(self) -> None: + super().__init__() + + self._mu_r = Parameter( + name='mu_r', + description='Absorption coefficient times sample radius (μR).', + display_handler=DisplayHandler( + display_name='μR', + latex_name=r'\mu R', + ), + value_spec=AttributeSpec( + default=0.0, + validator=RangeValidator(ge=0.0), + ), + cif_handler=CifHandler( + names=['_absorption.mu_r'], + iucr_name='_easydiffraction_absorption.mu_r', + ), + ) + + # ------------------------------------------------------------------ + # Public properties + # ------------------------------------------------------------------ + + @property + def mu_r(self) -> Parameter: + """ + Absorption coefficient times sample radius (μR). + + Reading this property returns the underlying ``Parameter`` + object. Assigning to it updates the parameter value. + """ + return self._mu_r + + @mu_r.setter + def mu_r(self, value: float) -> None: + self._mu_r.value = value diff --git a/src/easydiffraction/datablocks/experiment/categories/absorption/factory.py b/src/easydiffraction/datablocks/experiment/categories/absorption/factory.py new file mode 100644 index 000000000..7b03900c6 --- /dev/null +++ b/src/easydiffraction/datablocks/experiment/categories/absorption/factory.py @@ -0,0 +1,17 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause +"""Absorption factory — delegates entirely to ``FactoryBase``.""" + +from __future__ import annotations + +from typing import ClassVar + +from easydiffraction.core.factory import FactoryBase + + +class AbsorptionFactory(FactoryBase): + """Create sample-absorption correction models by tag.""" + + _default_rules: ClassVar[dict] = { + frozenset(): 'none', + } diff --git a/src/easydiffraction/datablocks/experiment/categories/absorption/none.py b/src/easydiffraction/datablocks/experiment/categories/absorption/none.py new file mode 100644 index 000000000..2b9d037cc --- /dev/null +++ b/src/easydiffraction/datablocks/experiment/categories/absorption/none.py @@ -0,0 +1,32 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause +"""No-op sample-absorption correction (the default).""" + +from __future__ import annotations + +from easydiffraction.core.metadata import CalculatorSupport +from easydiffraction.core.metadata import Compatibility +from easydiffraction.core.metadata import TypeInfo +from easydiffraction.datablocks.experiment.categories.absorption.base import AbsorptionBase +from easydiffraction.datablocks.experiment.categories.absorption.factory import AbsorptionFactory +from easydiffraction.datablocks.experiment.item.enums import AbsorptionTypeEnum +from easydiffraction.datablocks.experiment.item.enums import CalculatorEnum +from easydiffraction.datablocks.experiment.item.enums import SampleFormEnum +from easydiffraction.datablocks.experiment.item.enums import ScatteringTypeEnum + + +@AbsorptionFactory.register +class NoAbsorption(AbsorptionBase): + """No sample-absorption correction; the applied factor is unity.""" + + type_info = TypeInfo( + tag=AbsorptionTypeEnum.NONE.value, + description=AbsorptionTypeEnum.NONE.description(), + ) + compatibility = Compatibility( + sample_form=frozenset({SampleFormEnum.POWDER}), + scattering_type=frozenset({ScatteringTypeEnum.BRAGG}), + ) + calculator_support = CalculatorSupport( + calculators=frozenset({CalculatorEnum.CRYSPY, CalculatorEnum.CRYSFML}), + ) diff --git a/src/easydiffraction/datablocks/experiment/item/base.py b/src/easydiffraction/datablocks/experiment/item/base.py index 3588681c3..6f7d47a5d 100644 --- a/src/easydiffraction/datablocks/experiment/item/base.py +++ b/src/easydiffraction/datablocks/experiment/item/base.py @@ -11,6 +11,7 @@ import numpy as np from easydiffraction.core.datablock import DatablockItem +from easydiffraction.datablocks.experiment.categories.absorption.factory import AbsorptionFactory from easydiffraction.datablocks.experiment.categories.background.factory import BackgroundFactory from easydiffraction.datablocks.experiment.categories.calculator import CalculatorCategoryFactory from easydiffraction.datablocks.experiment.categories.data.factory import DataFactory @@ -93,6 +94,7 @@ def _attach_category_parents(self) -> None: getattr(self, '_diffrn', None), getattr(self, '_calculator_category', None), getattr(self, '_extinction', None), + getattr(self, '_absorption', None), getattr(self, '_linked_crystal', None), getattr(self, '_instrument', None), getattr(self, '_refln', None), @@ -114,6 +116,13 @@ def _supported_filters_for(self, category: object) -> dict[str, object]: return {'calculator': calculator} if category is getattr(self, '_extinction', None): return {'calculator': calculator} + if category is getattr(self, '_absorption', None): + return { + 'calculator': calculator, + 'sample_form': self.type.sample_form.value, + 'scattering_type': self.type.scattering_type.value, + 'beam_mode': self.type.beam_mode.value, + } if category is getattr(self, '_peak', None): return { 'calculator': calculator, @@ -243,6 +252,42 @@ def _replace_extinction( console.paragraph('Extinction type changed to') console.print(new_type) + def _swap_absorption(self, new_type: str) -> None: + """Switch the active absorption category.""" + self._replace_absorption(new_type, announce=True) + + def _replace_absorption( + self, + new_type: str, + *, + announce: bool, + strict: bool = True, + ) -> None: + """Replace the active absorption category.""" + supported = AbsorptionFactory.supported_for( + **self._supported_filters_for(self.absorption), + ) + supported_tags = [klass.type_info.tag for klass in supported] + if new_type not in supported_tags: + msg = ( + f"Unsupported absorption type '{new_type}'. " + f'Supported: {supported_tags}. ' + f"For more information, use 'absorption.show_supported()'" + ) + if strict: + raise ValueError(msg) + log.warning(msg) + return + + old_absorption = self._absorption + self._absorption = AbsorptionFactory.create(new_type) + old_absorption._parent = None + self._absorption._parent = self + self._absorption._type.value = new_type + if announce: + console.paragraph('Absorption type changed to') + console.print(new_type) + @property def name(self) -> str: """Human-readable name of the experiment.""" diff --git a/src/easydiffraction/datablocks/experiment/item/bragg_pd.py b/src/easydiffraction/datablocks/experiment/item/bragg_pd.py index bc3573d32..dbee4ff31 100644 --- a/src/easydiffraction/datablocks/experiment/item/bragg_pd.py +++ b/src/easydiffraction/datablocks/experiment/item/bragg_pd.py @@ -10,6 +10,7 @@ from easydiffraction.core.metadata import Compatibility from easydiffraction.core.metadata import TypeInfo +from easydiffraction.datablocks.experiment.categories.absorption.factory import AbsorptionFactory from easydiffraction.datablocks.experiment.categories.background.factory import BackgroundFactory from easydiffraction.datablocks.experiment.categories.instrument.factory import InstrumentFactory from easydiffraction.datablocks.experiment.categories.pref_orient.factory import PrefOrientFactory @@ -65,6 +66,7 @@ def __init__( self._instrument = InstrumentFactory.create(self._instrument_type) self._background = BackgroundFactory.create(BackgroundFactory.default_tag()) self._pref_orient = PrefOrientFactory.create(PrefOrientFactory.default_tag()) + self._absorption = AbsorptionFactory.create(AbsorptionFactory.default_tag()) self._refln = None self._sync_refln_category() self._attach_category_parents() @@ -198,6 +200,15 @@ def preferred_orientation(self) -> object: """Per-phase March-Dollase preferred-orientation corrections.""" return self._pref_orient + # ------------------------------------------------------------------ + # Absorption (switchable-category pattern, Bragg powder only) + # ------------------------------------------------------------------ + + @property + def absorption(self) -> object: + """Active sample-absorption correction for this experiment.""" + return self._absorption + def _restore_switchable_types(self, block: object) -> None: """ Restore Bragg powder switchable category types from CIF. @@ -206,3 +217,6 @@ def _restore_switchable_types(self, block: object) -> None: background_tag = read_cif_str(block, '_background.type') if background_tag is not None: self._replace_background(background_tag, announce=False, strict=False) + absorption_tag = read_cif_str(block, '_absorption.type') + if absorption_tag is not None: + self._replace_absorption(absorption_tag, announce=False, strict=False) diff --git a/src/easydiffraction/datablocks/experiment/item/enums.py b/src/easydiffraction/datablocks/experiment/item/enums.py index 079ad040b..6963b5e9b 100644 --- a/src/easydiffraction/datablocks/experiment/item/enums.py +++ b/src/easydiffraction/datablocks/experiment/item/enums.py @@ -272,3 +272,37 @@ def description(self) -> str: if self is ExtinctionModelEnum.LORENTZ: return 'Lorentzian mosaicity distribution for extinction correction.' return None + + +class AbsorptionTypeEnum(StrEnum): + """Sample-absorption correction types for powder experiments.""" + + NONE = 'none' + CYLINDER_HEWAT = 'cylinder-hewat' + + @classmethod + def default(cls) -> 'AbsorptionTypeEnum': + """ + Return the default absorption type (NONE). + + Returns + ------- + 'AbsorptionTypeEnum' + The default enum member. + """ + return cls.NONE + + def description(self) -> str: + """ + Return a human-readable description of this absorption type. + + Returns + ------- + str + Description string for the current enum member. + """ + if self is AbsorptionTypeEnum.NONE: + return 'No sample-absorption correction.' + if self is AbsorptionTypeEnum.CYLINDER_HEWAT: + return 'Cylindrical Debye-Scherrer absorption (Hewat).' + return None diff --git a/src/easydiffraction/io/cif/iucr_writer.py b/src/easydiffraction/io/cif/iucr_writer.py index da31df643..c6f9d7805 100644 --- a/src/easydiffraction/io/cif/iucr_writer.py +++ b/src/easydiffraction/io/cif/iucr_writer.py @@ -1276,6 +1276,7 @@ def _powder_extension_items(experiment: object) -> list[tuple[str, object]]: calculator = getattr(experiment, 'calculator', None) peak = getattr(experiment, 'peak', None) background = getattr(experiment, 'background', None) + absorption = getattr(experiment, 'absorption', None) items: list[tuple[str, object]] = [] items.extend( _iucr_items( @@ -1286,6 +1287,10 @@ def _powder_extension_items(experiment: object) -> list[tuple[str, object]]: items.extend(_iucr_items(calculator, ('type',))) items.extend(_iucr_items(peak, ('type',))) items.extend(_iucr_items(background, ('type',))) + items.extend(_iucr_items(absorption, ('type',))) + # ``mu_r`` exists only on the cylindrical Hewat absorption class. + if absorption is not None and hasattr(absorption, 'mu_r'): + items.extend(_iucr_items(absorption, ('mu_r',))) return items diff --git a/tests/unit/easydiffraction/analysis/calculators/test_absorption.py b/tests/unit/easydiffraction/analysis/calculators/test_absorption.py new file mode 100644 index 000000000..3a6165b18 --- /dev/null +++ b/tests/unit/easydiffraction/analysis/calculators/test_absorption.py @@ -0,0 +1,121 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + +import numpy as np +import pytest + + +class _FakeData: + def __init__(self, x): + self.x = x + + +class _FakeExperiment: + """Minimal stand-in exposing ``absorption`` and ``data.x``.""" + + def __init__(self, absorption, x): + self.absorption = absorption + self.data = _FakeData(x) + + +def _none(): + from easydiffraction.datablocks.experiment.categories.absorption.none import NoAbsorption + + return NoAbsorption() + + +def _hewat(mu_r): + from easydiffraction.datablocks.experiment.categories.absorption.cylinder_hewat import ( + CylinderHewatAbsorption, + ) + + absorption = CylinderHewatAbsorption() + absorption.mu_r = mu_r + return absorption + + +def test_module_import(): + import easydiffraction.analysis.calculators.absorption as MUT + + assert MUT.__name__.endswith('calculators.absorption') + + +def test_factor_none_is_unity(): + from easydiffraction.analysis.calculators import absorption + + two_theta = np.array([10.0, 50.0, 120.0]) + result = absorption.factor(two_theta, _none()) + assert np.allclose(result, 1.0) + + +def test_factor_hewat_matches_fullprof_to_four_decimals(): + # A(2theta=90, muR=0.7): theta=45deg, sin^2=0.5 + # exp(-(1.7133-0.0368*0.5)*0.7 + (0.0927+0.375*0.5)*0.49) ~ 0.35024 + from easydiffraction.analysis.calculators import absorption + + result = absorption.factor(np.array([90.0]), _hewat(0.7)) + assert result[0] == pytest.approx(0.35024, abs=1e-4) + + +def test_factor_hewat_is_unity_at_zero_mu_r(): + from easydiffraction.analysis.calculators import absorption + + result = absorption.factor(np.array([10.0, 90.0, 150.0]), _hewat(0.0)) + assert np.allclose(result, 1.0) + + +def test_factor_hewat_attenuates_low_angle_more(): + # The cylindrical correction is monotonically increasing in 2theta. + from easydiffraction.analysis.calculators import absorption + + result = absorption.factor(np.array([10.0, 90.0, 160.0]), _hewat(0.7)) + assert result[0] < result[1] < result[2] + + +def test_factor_warns_once_for_large_mu_r(monkeypatch): + from easydiffraction.analysis.calculators import absorption + + monkeypatch.setattr(absorption, '_WARNED_MU_R', set()) + calls = [] + monkeypatch.setattr(absorption.log, 'warning', lambda *a, **k: calls.append(a)) + + big = _hewat(2.0) # above HEWAT_MAX_VALIDATED_MU_R + absorption.factor(np.array([90.0]), big) + absorption.factor(np.array([90.0]), big) # same value: no second warning + assert len(calls) == 1 + + +def test_apply_multiplies_pattern(): + from easydiffraction.analysis.calculators import absorption + + x = np.array([10.0, 90.0, 150.0]) + y = np.array([100.0, 100.0, 100.0]) + expected = y * absorption.factor(x, _hewat(0.7)) + experiment = _FakeExperiment(_hewat(0.7), x) + assert np.allclose(absorption.apply(y, experiment), expected) + + +def test_apply_returns_unchanged_without_absorption(): + from easydiffraction.analysis.calculators import absorption + + class _NoAttr: + data = _FakeData(np.array([10.0, 20.0])) + + y = [1.0, 2.0] + assert absorption.apply(y, _NoAttr()) is y + + +def test_apply_returns_unchanged_for_empty_pattern(): + from easydiffraction.analysis.calculators import absorption + + experiment = _FakeExperiment(_hewat(0.7), np.array([10.0, 20.0])) + y = [] + assert absorption.apply(y, experiment) is y + + +def test_apply_returns_unchanged_on_length_mismatch(): + from easydiffraction.analysis.calculators import absorption + + experiment = _FakeExperiment(_hewat(0.7), np.array([10.0, 20.0, 30.0])) + y = np.array([1.0, 2.0]) # shorter than the 2-theta grid + assert absorption.apply(y, experiment) is y diff --git a/tests/unit/easydiffraction/analysis/calculators/test_crysfml.py b/tests/unit/easydiffraction/analysis/calculators/test_crysfml.py index a6a1371c8..ce4a4eda3 100644 --- a/tests/unit/easydiffraction/analysis/calculators/test_crysfml.py +++ b/tests/unit/easydiffraction/analysis/calculators/test_crysfml.py @@ -1,15 +1,71 @@ # SPDX-FileCopyrightText: 2025 EasyScience contributors # SPDX-License-Identifier: BSD-3-Clause +from types import SimpleNamespace + +import numpy as np import pytest +def _absorption_experiment_stub(x, mu_r): + """Minimal CWL experiment stub carrying a cylindrical absorption.""" + from easydiffraction.datablocks.experiment.categories.absorption.cylinder_hewat import ( + CylinderHewatAbsorption, + ) + from easydiffraction.datablocks.experiment.item.enums import BeamModeEnum + + absorption = CylinderHewatAbsorption() + absorption.mu_r = mu_r + return SimpleNamespace( + name='exp', + type=SimpleNamespace(beam_mode=SimpleNamespace(value=BeamModeEnum.CONSTANT_WAVELENGTH)), + absorption=absorption, + data=SimpleNamespace(x=np.asarray(x, dtype=float)), + ) + + def test_module_import(): import easydiffraction.analysis.calculators.crysfml as MUT assert MUT.__name__ == 'easydiffraction.analysis.calculators.crysfml' +def test_crysfml_calculate_pattern_applies_absorption(monkeypatch): + from easydiffraction.analysis.calculators import absorption + from easydiffraction.analysis.calculators.crysfml import CrysfmlCalculator + + calc = CrysfmlCalculator() + x = np.array([10.0, 90.0, 150.0]) + experiment = _absorption_experiment_stub(x, mu_r=0.7) + raw = [100.0, 100.0, 100.0] + monkeypatch.setattr(calc, '_crysfml_dict', lambda s, e: {}) + monkeypatch.setattr(calc, '_calculate_adjusted_pattern', lambda d, e: list(raw)) + + out = calc.calculate_pattern(None, experiment) + + expected = np.asarray(raw) * absorption.factor(x, experiment.absorption) + assert np.allclose(out, expected) + # The correction is non-trivial, so deleting the call site would fail. + assert not np.allclose(out, raw) + + +def test_crysfml_calculate_pattern_preserves_empty_no_data(monkeypatch): + from easydiffraction.analysis.calculators.crysfml import CrysfmlCalculator + + calc = CrysfmlCalculator() + experiment = _absorption_experiment_stub([10.0, 20.0], mu_r=0.7) + monkeypatch.setattr(calc, '_crysfml_dict', lambda s, e: {}) + + def _raise(_dict, _experiment): + msg = 'no calculated data' + raise KeyError(msg) + + monkeypatch.setattr(calc, '_calculate_adjusted_pattern', _raise) + + out = calc.calculate_pattern(None, experiment) + assert np.asarray(out).size == 0 + + def test_crysfml_engine_flag_and_structure_factors_raises(): from easydiffraction.analysis.calculators.crysfml import CrysfmlCalculator diff --git a/tests/unit/easydiffraction/analysis/calculators/test_cryspy.py b/tests/unit/easydiffraction/analysis/calculators/test_cryspy.py index bfa5c1db8..53658be69 100644 --- a/tests/unit/easydiffraction/analysis/calculators/test_cryspy.py +++ b/tests/unit/easydiffraction/analysis/calculators/test_cryspy.py @@ -486,3 +486,71 @@ def test_invalidate_stale_cache_drops_dict_on_pref_orient_axis_change(): experiment.preferred_orientation['lbco'].index_h = 1 calc._invalidate_stale_cache(combined_name, experiment, None) assert combined_name not in calc._cryspy_dicts + + +def _absorption_cwl_experiment_stub(x, mu_r): + """Minimal CWL experiment stub carrying a cylindrical absorption.""" + from easydiffraction.datablocks.experiment.categories.absorption.cylinder_hewat import ( + CylinderHewatAbsorption, + ) + from easydiffraction.datablocks.experiment.item.enums import BeamModeEnum + + absorption = CylinderHewatAbsorption() + absorption.mu_r = mu_r + return SimpleNamespace( + name='exp', + type=SimpleNamespace(beam_mode=SimpleNamespace(value=BeamModeEnum.CONSTANT_WAVELENGTH)), + absorption=absorption, + data=SimpleNamespace(x=np.asarray(x, dtype=float)), + ) + + +def _stub_cryspy_engine(monkeypatch, calc, block_payload): + """Stub the cryspy object build and engine call for pattern tests.""" + import easydiffraction.analysis.calculators.cryspy as cryspy_mod + + monkeypatch.setattr(calc, '_invalidate_stale_cache', lambda *a, **k: None) + monkeypatch.setattr( + calc, + '_recreate_cryspy_obj', + lambda s, e: SimpleNamespace(get_dictionary=lambda: {f'crystal_{s.name}': {}}), + ) + monkeypatch.setattr(calc, '_update_structure_in_cryspy_dict', lambda *a, **k: None) + monkeypatch.setattr(calc, '_update_experiment_in_cryspy_dict', lambda *a, **k: None) + + def _fake_rhochi(_dict, *, dict_in_out, **kwargs): + if block_payload is not None: + dict_in_out['pd_exp'] = block_payload + + monkeypatch.setattr(cryspy_mod, 'rhochi_calc_chi_sq_by_dictionary', _fake_rhochi) + + +def test_cryspy_calculate_pattern_applies_absorption(monkeypatch): + from easydiffraction.analysis.calculators import absorption + from easydiffraction.analysis.calculators.cryspy import CryspyCalculator + + calc = CryspyCalculator() + x = np.array([10.0, 90.0, 150.0]) + structure = SimpleNamespace(name='s') + experiment = _absorption_cwl_experiment_stub(x, mu_r=0.7) + raw = np.array([100.0, 100.0, 100.0]) + _stub_cryspy_engine(monkeypatch, calc, {'signal_plus': raw / 2, 'signal_minus': raw / 2}) + + out = calc.calculate_pattern(structure, experiment) + + expected = raw * absorption.factor(x, experiment.absorption) + assert np.allclose(out, expected) + # The correction is non-trivial, so deleting the call site would fail. + assert not np.allclose(out, raw) + + +def test_cryspy_calculate_pattern_no_data_returns_empty(monkeypatch): + from easydiffraction.analysis.calculators.cryspy import CryspyCalculator + + calc = CryspyCalculator() + structure = SimpleNamespace(name='s') + experiment = _absorption_cwl_experiment_stub(np.array([10.0, 20.0]), mu_r=0.7) + _stub_cryspy_engine(monkeypatch, calc, None) # no powder block -> KeyError path + + out = calc.calculate_pattern(structure, experiment) + assert list(out) == [] diff --git a/tests/unit/easydiffraction/datablocks/experiment/categories/absorption/test_base.py b/tests/unit/easydiffraction/datablocks/experiment/categories/absorption/test_base.py new file mode 100644 index 000000000..50ec8b552 --- /dev/null +++ b/tests/unit/easydiffraction/datablocks/experiment/categories/absorption/test_base.py @@ -0,0 +1,119 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + +import gemmi +import pytest + + +def test_module_import(): + import easydiffraction.datablocks.experiment.categories.absorption.base as MUT + + assert MUT.__name__.endswith('absorption.base') + + +def test_type_descriptor_cif_handler_names(): + from easydiffraction.datablocks.experiment.categories.absorption.none import NoAbsorption + + absorption = NoAbsorption() + assert '_absorption.type' in absorption._type._cif_handler.names + assert absorption._type._cif_handler.iucr_name == '_easydiffraction_absorption.type' + + +def test_absorption_exposed_on_bragg_powder_only(): + from easydiffraction import ExperimentFactory + + bragg = ExperimentFactory.from_scratch( + name='bragg', + sample_form='powder', + beam_mode='constant wavelength', + radiation_probe='neutron', + scattering_type='bragg', + ) + assert hasattr(bragg, 'absorption') + assert bragg.absorption.type == 'none' + assert bragg.absorption._parent is bragg + + total = ExperimentFactory.from_scratch( + name='total', + sample_form='powder', + beam_mode='constant wavelength', + radiation_probe='neutron', + scattering_type='total', + ) + assert not hasattr(total, 'absorption') + + +def test_switch_to_cylinder_hewat(): + from easydiffraction import ExperimentFactory + from easydiffraction.datablocks.experiment.categories.absorption.cylinder_hewat import ( + CylinderHewatAbsorption, + ) + + experiment = ExperimentFactory.from_scratch( + name='cwl', + sample_form='powder', + beam_mode='constant wavelength', + radiation_probe='neutron', + scattering_type='bragg', + ) + experiment.absorption.type = 'cylinder-hewat' + assert experiment.absorption.type == 'cylinder-hewat' + assert isinstance(experiment.absorption, CylinderHewatAbsorption) + + experiment.absorption.mu_r = 0.7 + assert experiment.absorption.mu_r.value == 0.7 + + +def test_cylinder_hewat_rejected_on_time_of_flight(): + from easydiffraction import ExperimentFactory + + experiment = ExperimentFactory.from_scratch( + name='tof', + sample_form='powder', + beam_mode='time-of-flight', + radiation_probe='neutron', + scattering_type='bragg', + ) + with pytest.raises(ValueError, match='absorption'): + experiment.absorption.type = 'cylinder-hewat' + assert experiment.absorption.type == 'none' + + +def test_from_cif_skips_type_descriptor(): + # The active type is restored by the owner's context-validated + # ``_restore_switchable_types``; the generic ``from_cif`` must not + # reapply ``_absorption.type``, or a rejected tag would desync the + # live category from its public selector. + from easydiffraction.datablocks.experiment.categories.absorption.cylinder_hewat import ( + CylinderHewatAbsorption, + ) + + doc = gemmi.cif.Document() + block = doc.add_new_block('test') + block.set_pair('_absorption.type', 'none') + block.set_pair('_absorption.mu_r', '0.5') + + absorption = CylinderHewatAbsorption() + absorption.from_cif(block) + + assert absorption.mu_r.value == 0.5 # non-type parameter is loaded + assert absorption.type == 'cylinder-hewat' # type descriptor skipped + + +def test_cif_round_trip_cylinder_hewat(): + from easydiffraction import ExperimentFactory + + experiment = ExperimentFactory.from_scratch( + name='lab6', + sample_form='powder', + beam_mode='constant wavelength', + radiation_probe='neutron', + scattering_type='bragg', + ) + experiment.absorption.type = 'cylinder-hewat' + experiment.absorption.mu_r = 0.7 + + restored = ExperimentFactory.from_cif_str(experiment.as_cif) + + assert restored.absorption.type == 'cylinder-hewat' + assert restored.absorption.mu_r.value == 0.7 diff --git a/tests/unit/easydiffraction/datablocks/experiment/categories/absorption/test_cylinder_hewat.py b/tests/unit/easydiffraction/datablocks/experiment/categories/absorption/test_cylinder_hewat.py new file mode 100644 index 000000000..7b7a7a6aa --- /dev/null +++ b/tests/unit/easydiffraction/datablocks/experiment/categories/absorption/test_cylinder_hewat.py @@ -0,0 +1,68 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + + +def test_module_import(): + import easydiffraction.datablocks.experiment.categories.absorption.cylinder_hewat as MUT + + assert MUT.__name__.endswith('absorption.cylinder_hewat') + + +def test_cylinder_hewat_type_info(): + from easydiffraction.datablocks.experiment.categories.absorption.cylinder_hewat import ( + CylinderHewatAbsorption, + ) + + assert CylinderHewatAbsorption.type_info.tag == 'cylinder-hewat' + assert CylinderHewatAbsorption.type_info.description != '' + + +def test_cylinder_hewat_mu_r_default_and_setter(): + from easydiffraction.datablocks.experiment.categories.absorption.cylinder_hewat import ( + CylinderHewatAbsorption, + ) + + absorption = CylinderHewatAbsorption() + assert absorption.mu_r.value == 0.0 + + absorption.mu_r = 0.7 + assert absorption.mu_r.value == 0.7 + + +def test_cylinder_hewat_mu_r_must_be_non_negative(monkeypatch): + from easydiffraction.datablocks.experiment.categories.absorption.cylinder_hewat import ( + CylinderHewatAbsorption, + ) + from easydiffraction.utils.logging import Logger + + monkeypatch.setattr(Logger, '_reaction', Logger.Reaction.WARN, raising=True) + + absorption = CylinderHewatAbsorption() + absorption.mu_r = 0.7 + absorption.mu_r = -0.1 # ge=0 -> rejected, keeps previous value + assert absorption.mu_r.value == 0.7 + + +def test_cylinder_hewat_mu_r_cif_handler_names(): + from easydiffraction.datablocks.experiment.categories.absorption.cylinder_hewat import ( + CylinderHewatAbsorption, + ) + + absorption = CylinderHewatAbsorption() + assert '_absorption.mu_r' in absorption._mu_r._cif_handler.names + assert absorption._mu_r._cif_handler.iucr_name == '_easydiffraction_absorption.mu_r' + + +def test_cylinder_hewat_is_constant_wavelength_only(): + from easydiffraction.datablocks.experiment.categories.absorption.cylinder_hewat import ( + CylinderHewatAbsorption, + ) + from easydiffraction.datablocks.experiment.item.enums import BeamModeEnum + from easydiffraction.datablocks.experiment.item.enums import SampleFormEnum + from easydiffraction.datablocks.experiment.item.enums import ScatteringTypeEnum + + compatibility = CylinderHewatAbsorption.compatibility + assert SampleFormEnum.POWDER in compatibility.sample_form + assert ScatteringTypeEnum.BRAGG in compatibility.scattering_type + assert BeamModeEnum.CONSTANT_WAVELENGTH in compatibility.beam_mode + assert BeamModeEnum.TIME_OF_FLIGHT not in compatibility.beam_mode diff --git a/tests/unit/easydiffraction/datablocks/experiment/categories/absorption/test_factory.py b/tests/unit/easydiffraction/datablocks/experiment/categories/absorption/test_factory.py new file mode 100644 index 000000000..94bba3ba0 --- /dev/null +++ b/tests/unit/easydiffraction/datablocks/experiment/categories/absorption/test_factory.py @@ -0,0 +1,70 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + + +def test_module_import(): + import easydiffraction.datablocks.experiment.categories.absorption.factory as MUT + + assert MUT.__name__.endswith('absorption.factory') + + +def test_factory_default_tag_is_none(): + from easydiffraction.datablocks.experiment.categories.absorption.factory import ( + AbsorptionFactory, + ) + + assert AbsorptionFactory.default_tag() == 'none' + + +def test_factory_supported_tags(): + from easydiffraction.datablocks.experiment.categories.absorption.factory import ( + AbsorptionFactory, + ) + + tags = AbsorptionFactory.supported_tags() + assert 'none' in tags + assert 'cylinder-hewat' in tags + + +def test_factory_create_returns_concrete_classes(): + from easydiffraction.datablocks.experiment.categories.absorption.cylinder_hewat import ( + CylinderHewatAbsorption, + ) + from easydiffraction.datablocks.experiment.categories.absorption.factory import ( + AbsorptionFactory, + ) + from easydiffraction.datablocks.experiment.categories.absorption.none import NoAbsorption + + assert isinstance(AbsorptionFactory.create('none'), NoAbsorption) + assert isinstance(AbsorptionFactory.create('cylinder-hewat'), CylinderHewatAbsorption) + + +def test_supported_for_cwl_powder_bragg_offers_both(): + from easydiffraction.datablocks.experiment.categories.absorption.factory import ( + AbsorptionFactory, + ) + + supported = AbsorptionFactory.supported_for( + calculator='cryspy', + sample_form='powder', + scattering_type='bragg', + beam_mode='constant wavelength', + ) + tags = {klass.type_info.tag for klass in supported} + assert tags == {'none', 'cylinder-hewat'} + + +def test_supported_for_tof_excludes_cylinder_hewat(): + from easydiffraction.datablocks.experiment.categories.absorption.factory import ( + AbsorptionFactory, + ) + + supported = AbsorptionFactory.supported_for( + calculator='cryspy', + sample_form='powder', + scattering_type='bragg', + beam_mode='time-of-flight', + ) + tags = {klass.type_info.tag for klass in supported} + assert 'cylinder-hewat' not in tags + assert 'none' in tags diff --git a/tests/unit/easydiffraction/datablocks/experiment/categories/absorption/test_none.py b/tests/unit/easydiffraction/datablocks/experiment/categories/absorption/test_none.py new file mode 100644 index 000000000..364cec950 --- /dev/null +++ b/tests/unit/easydiffraction/datablocks/experiment/categories/absorption/test_none.py @@ -0,0 +1,43 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + + +def test_module_import(): + import easydiffraction.datablocks.experiment.categories.absorption.none as MUT + + assert MUT.__name__.endswith('absorption.none') + + +def test_none_type_info(): + from easydiffraction.datablocks.experiment.categories.absorption.none import NoAbsorption + + assert NoAbsorption.type_info.tag == 'none' + assert NoAbsorption.type_info.description != '' + + +def test_none_has_no_mu_r_parameter(): + from easydiffraction.datablocks.experiment.categories.absorption.none import NoAbsorption + + absorption = NoAbsorption() + assert not hasattr(absorption, 'mu_r') + + +def test_none_identity_and_default_type(): + from easydiffraction.datablocks.experiment.categories.absorption.none import NoAbsorption + + absorption = NoAbsorption() + assert absorption._identity.category_code == 'absorption' + assert absorption.type == 'none' + + +def test_none_compatibility_and_calculator_support(): + from easydiffraction.datablocks.experiment.categories.absorption.none import NoAbsorption + from easydiffraction.datablocks.experiment.item.enums import CalculatorEnum + from easydiffraction.datablocks.experiment.item.enums import SampleFormEnum + from easydiffraction.datablocks.experiment.item.enums import ScatteringTypeEnum + + assert SampleFormEnum.POWDER in NoAbsorption.compatibility.sample_form + assert ScatteringTypeEnum.BRAGG in NoAbsorption.compatibility.scattering_type + assert NoAbsorption.calculator_support.supports(CalculatorEnum.CRYSPY) + assert NoAbsorption.calculator_support.supports(CalculatorEnum.CRYSFML) + assert not NoAbsorption.calculator_support.supports(CalculatorEnum.PDFFIT)