reciprocalspaceship 0.9.7__tar.gz → 1.0.7__tar.gz

reciprocalspaceship-1.0.7/PKG-INFO

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+Metadata-Version: 2.4
+Name: reciprocalspaceship
+Version: 1.0.7
+Summary: Tools for exploring reciprocal space
+Home-page: https://rs-station.github.io/reciprocalspaceship/
+Author: Kevin M. Dalton, Jack B. Greisman
+Author-email: kmdalton@g.harvard.edu, greisman@g.harvard.edu
+License: MIT
+Project-URL: Bug Tracker, https://github.com/rs-station/reciprocalspaceship/issues
+Project-URL: Documentation, https://rs-station.github.io/reciprocalspaceship/
+Project-URL: Source Code, https://github.com/rs-station/reciprocalspaceship
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Classifier: Topic :: Scientific/Engineering :: Physics
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Classifier: Programming Language :: Python
+Requires-Python: >=3.9
+License-File: LICENSE
+Requires-Dist: gemmi<=0.7.3,>=0.7.0
+Requires-Dist: pandas<=2.3.3,>=2.2.2
+Requires-Dist: numpy
+Requires-Dist: scipy
+Requires-Dist: ipython
+Requires-Dist: msgpack
+Requires-Dist: setuptools
+Requires-Dist: joblib
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+Requires-Dist: pytest-xdist; extra == "dev"
+Provides-Extra: doc
+Requires-Dist: sphinx; extra == "doc"
+Requires-Dist: sphinx_rtd_theme; extra == "doc"
+Requires-Dist: nbsphinx; extra == "doc"
+Requires-Dist: sphinx-design; extra == "doc"
+Requires-Dist: sphinxcontrib-autoprogram; extra == "doc"
+Requires-Dist: autodocsumm; extra == "doc"
+Requires-Dist: jupyter; extra == "doc"
+Requires-Dist: tqdm; extra == "doc"
+Requires-Dist: matplotlib; extra == "doc"
+Requires-Dist: seaborn; extra == "doc"
+Requires-Dist: celluloid; extra == "doc"
+Requires-Dist: scikit-image; extra == "doc"
+Provides-Extra: examples
+Requires-Dist: jupyter; extra == "examples"
+Requires-Dist: tqdm; extra == "examples"
+Requires-Dist: matplotlib; extra == "examples"
+Requires-Dist: seaborn; extra == "examples"
+Requires-Dist: celluloid; extra == "examples"
+Requires-Dist: scikit-image; extra == "examples"
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: home-page
+Dynamic: license
+Dynamic: license-file
+Dynamic: project-url
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
+
+
+``reciprocalspaceship`` provides a ``pandas``-style interface for
+analyzing and manipulating reflection data from crystallography
+experiments. Using this library, it is possible to interactively work
+with crystallographic data in Python, enabling easy integration  with
+modern scientific computing libraries. ``reciprocalspaceship`` is
+intended to support the rapid prototyping of new crystallographic methods
+and custom analyses while maintaining clear, reproducible, and performant
+code.
+
+Features of this library include:
+
+  - Crystallographically-aware ``pandas`` objects, datatypes, and syntax
+    that are familiar to Python users.
+  - Convenient integration with `GEMMI <https://gemmi.readthedocs.io/en/latest/>`__
+    to provide built-in methods and support for developing functions that
+    use space groups, unit cell parameters, and crystallographic symmetry
+    operations.
+  - Support for reading and writing MTZ reflection files.

reciprocalspaceship-1.0.7/README.md

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+# 1 / 🚀 = reciprocalspaceship
+![Build](https://github.com/rs-station/reciprocalspaceship/workflows/Build/badge.svg)
+[![Documentation](https://github.com/rs-station/reciprocalspaceship/workflows/Documentation/badge.svg)](https://rs-station.github.io/reciprocalspaceship)
+[![PyPI](https://img.shields.io/pypi/v/reciprocalspaceship?color=blue)](https://pypi.org/project/reciprocalspaceship/)
+[![Anaconda-Server Badge](https://anaconda.org/conda-forge/reciprocalspaceship/badges/version.svg)](https://anaconda.org/conda-forge/reciprocalspaceship)
+[![codecov](https://codecov.io/gh/rs-station/reciprocalspaceship/branch/main/graph/badge.svg)](https://codecov.io/gh/rs-station/reciprocalspaceship)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://github.com/rs-station/reciprocalspaceship/blob/main/LICENSE)
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/rs-station/reciprocalspaceship/main?filepath=docs%2Fexamples)
+[![DOI](https://img.shields.io/badge/DOI-10.1107%2FS160057672100755X-blue)](https://doi.org/10.1107/S160057672100755X)
+
+Tools for exploring reciprocal space.
+
+`reciprocalspaceship` provides a `pandas`-style interface for
+analyzing and manipulating reflection data from crystallography
+experiments. Using this library, it is possible to interactively
+work with crystallographic data in Python, enabling easy
+integration with modern scientific computing libraries. `reciprocalspaceship`
+is intended to support the rapid prototyping of new crystallographic methods and
+custom analyses while maintaining clear and performant code.
+
+Features of this library include:
+
+- Crystallographically-aware `pandas` objects, datatypes, and syntax that are familiar to Python users.
+- Convenient integration with [GEMMI](https://gemmi.readthedocs.io/en/latest/) to provide built-in methods and
+  support for developing functions that use space groups, unit cell parameters, and crystallographic
+  symmetry operations.
+- Support for reading and writing MTZ reflection files.
+
+<p align="center">
+  <img src="docs/img/screenshot.png" width=750 title="Screenshot of Jupyter Notebook">
+</p>
+
+## Installation
+
+The fastest way to install `reciprocalspaceship` is using `pip`:
+
+```
+pip install reciprocalspaceship
+```
+
+or using `conda`:
+
+```
+conda install -c conda-forge reciprocalspaceship
+```
+
+For more installation information, see our [installation guide](https://rs-station.github.io/reciprocalspaceship/userguide/installation.html).
+
+## Quickstart
+
+To get started with `reciprocalspaceship`, see our [quickstart guide](https://rs-station.github.io/reciprocalspaceship/examples/quickstart.html).
+
+## Documentation
+
+For more details on the use of `reciprocalspaceship`, check out our [documentation](https://rs-station.github.io/reciprocalspaceship).
+
+## Reference
+
+Our paper describing the library was published in the Journal of Applied Crystallography: [link to paper](https://doi.org/10.1107/S160057672100755X).
+Please cite this publication for any work that makes use of this library.
+
+We also have a pre-print describing the library on [bioRxiv](https://www.biorxiv.org/content/10.1101/2021.02.03.429617v1).

reciprocalspaceship-1.0.7/reciprocalspaceship/VERSION

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+1.0.7

reciprocalspaceship-1.0.7/reciprocalspaceship/__init__.py

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+# Version number for reciprocalspaceship
+def getVersionNumber():
+    version = None
+    try:
+        from setuptools.version import metadata
+
+        version = metadata.version("reciprocalspaceship")
+    except ImportError:
+        from setuptools.version import pkg_resources
+
+        version = pkg_resources.require("reciprocalspaceship")[0].version
+
+    return version
+
+
+__version__ = getVersionNumber()
+
+# Import submodules
+from reciprocalspaceship import algorithms, stats
+
+# Top-Level API
+from reciprocalspaceship.concat import concat
+from reciprocalspaceship.dataseries import DataSeries
+from reciprocalspaceship.dataset import DataSet
+
+# Add support for MTZ data types:
+# see http://www.ccp4.ac.uk/html/f2mtz.html
+from reciprocalspaceship.dtypes import AnomalousDifferenceDtype  # D
+from reciprocalspaceship.dtypes import BatchDtype  # B
+from reciprocalspaceship.dtypes import FriedelIntensityDtype  # K
+from reciprocalspaceship.dtypes import FriedelStructureFactorAmplitudeDtype  # G
+from reciprocalspaceship.dtypes import HendricksonLattmanDtype  # A
+from reciprocalspaceship.dtypes import HKLIndexDtype  # H
+from reciprocalspaceship.dtypes import IntensityDtype  # J
+from reciprocalspaceship.dtypes import M_IsymDtype  # Y
+from reciprocalspaceship.dtypes import MTZIntDtype  # I
+from reciprocalspaceship.dtypes import MTZRealDtype  # R
+from reciprocalspaceship.dtypes import NormalizedStructureFactorAmplitudeDtype  # E
+from reciprocalspaceship.dtypes import PhaseDtype  # P
+from reciprocalspaceship.dtypes import StandardDeviationDtype  # Q
+from reciprocalspaceship.dtypes import StandardDeviationFriedelIDtype  # M
+from reciprocalspaceship.dtypes import StandardDeviationFriedelSFDtype  # L
+from reciprocalspaceship.dtypes import StructureFactorAmplitudeDtype  # F
+from reciprocalspaceship.dtypes import WeightDtype  # W
+from reciprocalspaceship.dtypes import summarize_mtz_dtypes
+from reciprocalspaceship.io import (
+    read_cif,
+    read_crystfel,
+    read_csv,
+    read_mtz,
+    read_pickle,
+    read_precognition,
+)

reciprocalspaceship-1.0.7/reciprocalspaceship/algorithms/__init__.py

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+from reciprocalspaceship.algorithms.intensity import (
+    compute_intensity_from_structurefactor,
+)
+from reciprocalspaceship.algorithms.merge import merge
+from reciprocalspaceship.algorithms.scale_merged_intensities import (
+    scale_merged_intensities,
+)

reciprocalspaceship-1.0.7/reciprocalspaceship/algorithms/intensity.py

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+import numpy as np
+
+import reciprocalspaceship as rs
+from reciprocalspaceship.decorators import inplace
+
+
+@inplace
+def compute_intensity_from_structurefactor(
+    ds,
+    F_key,
+    SigF_key,
+    output_columns=None,
+    inplace=False,
+):
+    """
+    Compute intensities (I) and uncertainty estimates (SigI) from structure
+    factor amplitudes (F) and their uncertainties (SigF) using error propagation
+
+    Intensity computed as I = SigF*SigF + F*F. Intensity error estimate
+    approximated as SigI = abs(2*F*SigF)
+
+    Parameters
+    ----------
+    ds : DataSet
+        Input DataSet containing columns with F_key and SigF_key labels
+    F_key : str
+        Column label for structure factor amplitudes
+    SigF_key : str
+        Column label for structure factor error estimates
+    output_columns : list or tuple of column names
+        Column labels to be added to ds for calculated I and
+        SigI, respectively. output_columns must have len=2.
+    inplace : bool
+        Whether to modify the DataSet in place or create a copy
+
+    Returns
+    -------
+    DataSet
+        DataSet with 2 additional columns corresponding to calculated
+        intensities and intensity error estimates
+
+    """
+
+    if output_columns is None:
+        output_columns = ["I_calc", "SigI_calc"]
+    (
+        I_key,
+        SigI_key,
+    ) = output_columns
+
+    if I_key in ds.columns:
+        raise ValueError(
+            f"Input {ds.__class__.__name__} already contains column '{I_key}'."
+            f"Try again and use the output_columns argument to pick a new"
+            f"output column name."
+        )
+    if SigI_key in ds.columns:
+        raise ValueError(
+            f"Input {ds.__class__.__name__} already contains column '{SigI_key}'."
+            f"Try again and use the output_columns argument to pick a new"
+            f"output column name."
+        )
+
+    # Confirm F_key and SigF_key are of the correct dtype
+    if not isinstance(ds.dtypes[F_key], rs.StructureFactorAmplitudeDtype):
+        raise ValueError(
+            f"Column {F_key} is not of type rs.StructureFactorAmplitudeDtype."
+            f"Try again and provide structure factor amplitudes for F_key"
+        )
+    if not isinstance(ds.dtypes[SigF_key], rs.StandardDeviationDtype):
+        raise ValueError(
+            f"Column {SigF_key} is not of type rs.StandardDeviationDtype."
+            f"Try again and provide standard deviations for SigF_key"
+        )
+
+    # Initialize outputs
+    ds[I_key] = (ds[F_key] * ds[F_key] + ds[SigF_key] * ds[SigF_key]).astype(
+        "Intensity"
+    )
+    ds[SigI_key] = (2 * ds[F_key] * ds[SigF_key]).abs().astype("Stddev")
+
+    return ds

reciprocalspaceship-1.0.7/reciprocalspaceship/algorithms/merge.py

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+import numpy as np
+
+
+def merge(dataset, intensity_key="I", sigma_key="SIGI", anomalous=True, sort=False):
+    """
+    Merge dataset using inverse-variance weights.
+
+    Parameters
+    ----------
+    dataset : rs.DataSet
+        Unmerged DataSet containing scaled intensities and uncertainties
+    intensity_key : str (optional)
+        Column name for intensities
+    sigma_key : str (optional)
+        Column name for uncertainties
+    anomalous : bool (optional)
+        If True, do not merge Friedel mates
+    sort : bool (optional)
+        If True, index of returned DataSet will be sorted
+
+    Returns
+    -------
+    rs.DataSet
+        Merged DataSet object
+    """
+
+    if dataset.merged:
+        raise ValueError(
+            "rs.algorithms.merge() can only be called with an unmerged DataSet"
+        )
+
+    # Map observations to reciprocal ASU
+    ds = dataset.hkl_to_asu(anomalous=anomalous)
+    ds["w"] = ds[sigma_key] ** -2
+    ds["wI"] = ds[intensity_key] * ds["w"]
+    g = ds.groupby(["H", "K", "L"])
+
+    result = g[["w", "wI"]].sum()
+    result["I"] = result["wI"] / result["w"]
+    result["SIGI"] = np.sqrt(1 / result["w"]).astype("Stddev")
+    result["N"] = g.size()
+    result.merged = True
+
+    # Reshape anomalous data and use to compute IMEAN / SIGIMEAN
+    if anomalous:
+        result = result.unstack_anomalous()
+        result.loc[:, ["N(+)", "N(-)"]] = result[["N(+)", "N(-)"]].fillna(0).astype("I")
+        result["IMEAN"] = result[["wI(+)", "wI(-)"]].sum(axis=1) / result[
+            ["w(+)", "w(-)"]
+        ].sum(axis=1).astype("Intensity")
+        result["SIGIMEAN"] = np.sqrt(1 / (result[["w(+)", "w(-)"]].sum(axis=1))).astype(
+            "Stddev"
+        )
+
+        # Adjust SIGIMEAN for centric reflections due to duplicated values in
+        # Friedel columns
+        centrics = result.label_centrics()["CENTRIC"]
+        result.loc[centrics, "SIGIMEAN"] *= np.sqrt(2)
+
+        result = result[
+            ["IMEAN", "SIGIMEAN", "I(+)", "SIGI(+)", "I(-)", "SIGI(-)", "N(+)", "N(-)"]
+        ]
+    else:
+        result = result[["I", "SIGI", "N"]]
+
+    if sort:
+        return result.sort_index()
+
+    return result