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Fix peak profile function and parameter names (#150)
* Apply latest templates * Correcting peak profiles * Make load_numeric_block skip non-numeric lines anywhere in file * Add double-jorgensen-von-dreele peak profile (CrysPy type0m) * Add some temporary documents and tests [ci skip] * Clean up * Exclude tmp/ directory and update roadmap * Clean up
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‎.copier-answers.yml‎

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# WARNING: Do not edit this file manually.
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# Any changes will be overwritten by Copier.
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_commit: v0.10.1-40-g29e2ccf
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_commit: v0.10.1-41-g508666e
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_src_path: gh:easyscience/templates
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app_docs_url: https://easyscience.github.io/diffraction-app
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app_doi: 10.5281/zenodo.18163581

‎.github/workflows/pypi-test.yml‎

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run: pixi init easydiffraction
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- name: Set the minimum system requirements
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working-directory: easydiffraction
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run: pixi project system-requirements add macos 14.0
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- name: Add Python 3.14 from Conda

‎.github/workflows/test.yml‎

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echo
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echo "🔹🔸🔹🔸🔹 Python: $py_ver 🔹🔸🔹🔸🔹"
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env="py-$(echo $py_ver | tr -d .)-env" # Converts 3.11 -> py-311-env
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env="py-$(echo $py_ver | tr -d .)-env" # Converts 3.XX -> py-3XX-env
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echo "Running tests in environment: $env"
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pixi run --environment $env unit-tests
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done
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- name: Run functional tests
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shell: bash
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run: |
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set -euo pipefail
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for py_ver in $PY_VERSIONS; do
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echo
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echo "🔹🔸🔹🔸🔹 Python: $py_ver 🔹🔸🔹🔸🔹"
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env="py-$(echo $py_ver | tr -d .)-env" # Converts 3.XX -> py-3XX-env
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echo "Running tests in environment: $env"
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pixi run --environment $env functional-tests
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done
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- name: Run integration tests ${{ needs.env-prepare.outputs.pytest-marks }}
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shell: bash
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run: |
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echo
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echo "🔹🔸🔹🔸🔹 Python: $py_ver 🔹🔸🔹🔸🔹"
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env="py-$(echo $py_ver | tr -d .)-env" # Converts 3.11 -> py-311-env
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env="py-$(echo $py_ver | tr -d .)-env" # Converts 3.XX -> py-3XX-env
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echo "Running tests in environment: $env"
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pixi run --environment $env integration-tests ${{ needs.env-prepare.outputs.pytest-marks }}
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cd ..
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done
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- name: Run functional tests
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shell: bash
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run: |
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set -euo pipefail
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for py_ver in $PY_VERSIONS; do
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echo
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echo "🔹🔸🔹🔸🔹 Python: $py_ver 🔹🔸🔹🔸🔹"
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echo "Entering pixi project directory easydiffraction_py$py_ver"
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cd easydiffraction_py$py_ver
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echo "Running tests"
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pixi run python -m pytest ../tests/functional/ --color=yes -v
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echo "Exiting pixi project directory"
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cd ..
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done
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- name: Run integration tests ${{ needs.env-prepare.outputs.pytest-marks }}
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shell: bash
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run: |

‎.gitignore‎

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# Used to fetch tutorials data during their runtime. Need to have '/' at
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# the beginning to avoid ignoring 'data' module in the src/.
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/data/
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/tmp/

‎docs/architecture/ROADMAP.md‎

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### Atomic Displacement Parameters (ADP)
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| Feature | LIB | APP |
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| ----------------------------------------------- | ----------- | --- |
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| Isotropic Biso | ✅ | 🗓 |
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| Isotropic Uiso | 🗓 | ✅ |
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| Anisotropic Bani _B11, B22, B33, B12, B13, B23_ | 🗓`highest` | 🗓 |
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| Anisotropic Uani _U11, U22, U33, U12, U13, U23_ | 🗓 | 🗓 |
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| Feature | LIB | APP |
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| ----------------------------------------------- | --- | --- |
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| Isotropic Biso | ✅ | 🗓 |
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| Isotropic Uiso | 🚧 | ✅ |
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| Anisotropic Bani _B11, B22, B33, B12, B13, B23_ | 🚧 | 🗓 |
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| Anisotropic Uani _U11, U22, U33, U12, U13, U23_ | 🚧 | 🗓 |
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---
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| Feature | LIB | APP |
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| -------------------------------------------------------- | --- | --- |
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| Wavelength | ✅ | ✅ |
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| Second wavelength | 🚧 | 🗓 |
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| Second wavelength | 🗓 | 🗓 |
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| 2θ offset | ✅ | ✅ |
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| Sample displacement correction (FullProf _SyCos, SySin_) | 🚧 | 🗓 |
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| Sample displacement correction (FullProf _SyCos, SySin_) | 🗓 | 🗓 |
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### Instrument — Time-of-Flight
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### Peak Profile — Constant Wavelength
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CrysPy: Pseudo-Voigt from FullProf. Empirical asymmetry, 4 params (p1,
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p2, p3, p4) from FullProf.
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| Feature | LIB | APP |
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| ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ----- | --- |
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| Pseudo-Voigt + Empirical asymmetry<br>_Gaussian broadening U, V, W. Lorentzian broadening X, Y<br>Empirical asymmetry p1, p2, p3, p4_<br>(CrysPy) | ✅ | ✅ |
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| Feature | LIB | APP |
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| ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | --- | --- |
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| Jorgensen (back-to-back exponentials ⊗ Gaussian)<br>_Gaussian broadening σ₀, σ₁, σ₂<br>Back-to-back exponential rise α₀, α₁. Back-to-back exponential decay β₀, β₁_<br>(CrysPy) | ✅ | ✅ |
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| Jorgensen-Von Dreele (back-to-back exponentials ⊗ pseudo-Voigt)<br>_Gaussian broadening σ₀, σ₁, σ₂. Lorentzian broadening γ₀, γ₁, γ₂<br>Back-to-back exponential rise α₀, α₁. Back-to-back exponential decay β₀, β₁_<br>(CrysPy) | 🗓 | ✅ |
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| Double back-to-back exponentials ⊗ pseudo-Voigt [Z-Rietveld type0m]<br>_Gaussian broadening σ₀, σ₁, σ₂. Lorentzian broadening γ₀, γ₁, γ₂<br>Rise α₁, α₂. Fast decay β₀₀, β₀₁. Slow decay β₁₀. Switching r₀₁, r₀₂, r₀₃_<br>(CrysPy) | 🗓 | 🗓 |
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| Jorgensen-Von Dreele (back-to-back exponentials ⊗ pseudo-Voigt)<br>_Gaussian broadening σ₀, σ₁, σ₂. Lorentzian broadening γ₀, γ₁, γ₂<br>Back-to-back exponential rise α₀, α₁. Back-to-back exponential decay β₀, β₁_<br>(CrysPy) | ✅ | ✅ |
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| Double back-to-back exponentials ⊗ pseudo-Voigt [Z-Rietveld type0m]<br>_Gaussian broadening σ₀, σ₁, σ₂. Lorentzian broadening γ₀, γ₁, γ₂<br>Rise α₁, α₂. Fast decay β₀₀, β₀₁. Slow decay β₁₀. Switching r₀₁, r₀₂, r₀₃_<br>(CrysPy) | ✅ | 🗓 |
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| Ikeda-Carpenter ⊗ pseudo-Voigt<br>_Moderator pulse α₀, α₁, β₀, κ<br>Gaussian broadening σ². Lorentzian broadening γ_<br>(CrysFML) | 🗓 | 🗓 |
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| TOF profile | TOF source | Performance |
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| ------------------------------------------------------------------- | ----------------------------------------------------------------- | ----------- |
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| Jorgensen (back-to-back exponentials ⊗ Gaussian) | Simpler TOF profile, including reactor-source TOF implementations | Fast |
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| Jorgensen-Von Dreele (back-to-back exponentials ⊗ pseudo-Voigt) | Spallation-source TOF | Slower |
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| Double back-to-back exponentials ⊗ pseudo-Voigt (Z-Rietveld type0m) | Spallation-source TOF; more elaborate asymmetric profile | Slowest |
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| Ikeda-Carpenter ⊗ pseudo-Voigt | Spallation-source TOF; moderator pulse shape model | Moderate |
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---
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### Extinction
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CrysPy's extinction is NOT Shelx-style. It's an analytical
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Becker-Coppens spherical model with Gauss or Lorentz mosaicity
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distribution
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CrysPy's extinction is an analytical Becker-Coppens spherical model with
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Gauss or Lorentz mosaicity distribution
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| Feature | LIB | APP |
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| ----------------------------------------------------- | --- | --- |

‎docs/architecture/architecture.md‎

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frozenset({
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('scattering_type', ScatteringTypeEnum.BRAGG),
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('beam_mode', BeamModeEnum.TIME_OF_FLIGHT),
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}): PeakProfileTypeEnum.PSEUDO_VOIGT_IKEDA_CARPENTER,
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}): PeakProfileTypeEnum.JORGENSEN,
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frozenset({
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('scattering_type', ScatteringTypeEnum.TOTAL),
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}): PeakProfileTypeEnum.GAUSSIAN_DAMPED_SINC,
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### 5.5 All Factories
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| Factory | Domain | Tags resolve to |
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| ---------------------------- | ---------------------- | ----------------------------------------------------------- |
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| `BackgroundFactory` | Background categories | `LineSegmentBackground`, `ChebyshevPolynomialBackground` |
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| `PeakFactory` | Peak profiles | `CwlPseudoVoigt`, `TofPseudoVoigtIkedaCarpenter`, … |
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| `InstrumentFactory` | Instruments | `CwlPdInstrument`, `TofPdInstrument`, … |
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| `DataFactory` | Data collections | `PdCwlData`, `PdTofData`, `ReflnData`, `TotalData` |
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| `ExtinctionFactory` | Extinction models | `BeckerCoppensExtinction` |
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| `LinkedCrystalFactory` | Linked-crystal refs | `LinkedCrystal` |
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| `ExcludedRegionsFactory` | Excluded regions | `ExcludedRegions` |
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| `LinkedPhasesFactory` | Linked phases | `LinkedPhases` |
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| `ExperimentTypeFactory` | Experiment descriptors | `ExperimentType` |
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| `CellFactory` | Unit cells | `Cell` |
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| `SpaceGroupFactory` | Space groups | `SpaceGroup` |
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| `AtomSitesFactory` | Atom sites | `AtomSites` |
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| `AliasesFactory` | Parameter aliases | `Aliases` |
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| `ConstraintsFactory` | Parameter constraints | `Constraints` |
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| `FitModeFactory` | Fit-mode category | `FitMode` |
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| `JointFitExperimentsFactory` | Joint-fit weights | `JointFitExperiments` |
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| `CalculatorFactory` | Calculation engines | `CryspyCalculator`, `CrysfmlCalculator`, `PdffitCalculator` |
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| `MinimizerFactory` | Minimisers | `LmfitMinimizer`, `DfolsMinimizer`, … |
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| Factory | Domain | Tags resolve to |
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| ---------------------------- | ---------------------- | ------------------------------------------------------------ |
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| `BackgroundFactory` | Background categories | `LineSegmentBackground`, `ChebyshevPolynomialBackground` |
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| `PeakFactory` | Peak profiles | `CwlPseudoVoigt`, `TofJorgensen`, `TofJorgensenVonDreele`, … |
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| `InstrumentFactory` | Instruments | `CwlPdInstrument`, `TofPdInstrument`, … |
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| `DataFactory` | Data collections | `PdCwlData`, `PdTofData`, `ReflnData`, `TotalData` |
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| `ExtinctionFactory` | Extinction models | `BeckerCoppensExtinction` |
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| `LinkedCrystalFactory` | Linked-crystal refs | `LinkedCrystal` |
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| `ExcludedRegionsFactory` | Excluded regions | `ExcludedRegions` |
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| `LinkedPhasesFactory` | Linked phases | `LinkedPhases` |
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| `ExperimentTypeFactory` | Experiment descriptors | `ExperimentType` |
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| `CellFactory` | Unit cells | `Cell` |
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| `SpaceGroupFactory` | Space groups | `SpaceGroup` |
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| `AtomSitesFactory` | Atom sites | `AtomSites` |
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| `AliasesFactory` | Parameter aliases | `Aliases` |
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| `ConstraintsFactory` | Parameter constraints | `Constraints` |
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| `FitModeFactory` | Fit-mode category | `FitMode` |
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| `JointFitExperimentsFactory` | Joint-fit weights | `JointFitExperiments` |
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| `CalculatorFactory` | Calculation engines | `CryspyCalculator`, `CrysfmlCalculator`, `PdffitCalculator` |
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| `MinimizerFactory` | Minimisers | `LmfitMinimizer`, `DfolsMinimizer`, … |
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> **Note:** `ExperimentFactory` and `StructureFactory` are _builder_
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> factories with `from_cif_path`, `from_cif_str`, `from_data_path`, and
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**Peak tags**
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| Tag | Class |
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| ---------------------------------- | ------------------------------ |
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| `pseudo-voigt` | `CwlPseudoVoigt` |
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| `split-pseudo-voigt` | `CwlSplitPseudoVoigt` |
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| `thompson-cox-hastings` | `CwlThompsonCoxHastings` |
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| `tof-pseudo-voigt` | `TofPseudoVoigt` |
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| `tof-pseudo-voigt-ikeda-carpenter` | `TofPseudoVoigtIkedaCarpenter` |
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| `tof-pseudo-voigt-back-to-back` | `TofPseudoVoigtBackToBack` |
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| `gaussian-damped-sinc` | `TotalGaussianDampedSinc` |
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| Tag | Class |
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| ------------------------------------ | ---------------------------------- |
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| `pseudo-voigt` | `CwlPseudoVoigt` |
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| `pseudo-voigt + empirical asymmetry` | `CwlPseudoVoigtEmpiricalAsymmetry` |
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| `thompson-cox-hastings` | `CwlThompsonCoxHastings` |
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| `jorgensen` | `TofJorgensen` |
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| `jorgensen-von-dreele` | `TofJorgensenVonDreele` |
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| `double-jorgensen-von-dreele` | `TofDoubleJorgensenVonDreele` |
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| `gaussian-damped-sinc` | `TotalGaussianDampedSinc` |
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**Instrument tags**
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#### Singleton CategoryItems — factory-created (get all three)
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| Class | Factory |
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| ------------------------------ | ----------------------- |
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| `CwlPdInstrument` | `InstrumentFactory` |
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| `CwlScInstrument` | `InstrumentFactory` |
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| `TofPdInstrument` | `InstrumentFactory` |
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| `TofScInstrument` | `InstrumentFactory` |
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| `CwlPseudoVoigt` | `PeakFactory` |
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| `CwlSplitPseudoVoigt` | `PeakFactory` |
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| `CwlThompsonCoxHastings` | `PeakFactory` |
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| `TofPseudoVoigt` | `PeakFactory` |
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| `TofPseudoVoigtIkedaCarpenter` | `PeakFactory` |
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| `TofPseudoVoigtBackToBack` | `PeakFactory` |
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| `TotalGaussianDampedSinc` | `PeakFactory` |
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| `BeckerCoppensExtinction` | `ExtinctionFactory` |
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| `LinkedCrystal` | `LinkedCrystalFactory` |
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| `Cell` | `CellFactory` |
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| `SpaceGroup` | `SpaceGroupFactory` |
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| `ExperimentType` | `ExperimentTypeFactory` |
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| `FitMode` | `FitModeFactory` |
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| Class | Factory |
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| ---------------------------------- | ----------------------- |
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| `CwlPdInstrument` | `InstrumentFactory` |
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| `CwlScInstrument` | `InstrumentFactory` |
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| `TofPdInstrument` | `InstrumentFactory` |
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| `TofScInstrument` | `InstrumentFactory` |
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| `CwlPseudoVoigt` | `PeakFactory` |
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| `CwlPseudoVoigtEmpiricalAsymmetry` | `PeakFactory` |
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| `CwlThompsonCoxHastings` | `PeakFactory` |
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| `TofJorgensen` | `PeakFactory` |
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| `TofJorgensenVonDreele` | `PeakFactory` |
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| `TofDoubleJorgensenVonDreele` | `PeakFactory` |
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| `TotalGaussianDampedSinc` | `PeakFactory` |
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| `BeckerCoppensExtinction` | `ExtinctionFactory` |
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| `LinkedCrystal` | `LinkedCrystalFactory` |
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| `Cell` | `CellFactory` |
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| `SpaceGroup` | `SpaceGroupFactory` |
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| `ExperimentType` | `ExperimentTypeFactory` |
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| `FitMode` | `FitModeFactory` |
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#### CategoryCollections — factory-created (get all three)
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)
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expt.instrument.calib_d_to_tof_offset = 0.0
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expt.instrument.calib_d_to_tof_linear = 7476.91
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expt.peak_profile_type = 'pseudo-voigt * ikeda-carpenter'
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expt.peak_profile_type = 'jorgensen'
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expt.peak.broad_gauss_sigma_0 = 3.0
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```
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