reciprocalspaceship 1.0.1__py3-none-any.whl → 1.0.3__py3-none-any.whl

reciprocalspaceship/io/dials.py

@@ -0,0 +1,330 @@
+import logging
+import sys
+
+import msgpack
+import numpy as np
+import pandas
+
+LOGGER = logging.getLogger("rs.io.dials")
+if not LOGGER.handlers:
+    LOGGER.setLevel(logging.DEBUG)
+    console = logging.StreamHandler(stream=sys.stdout)
+    console.setLevel(logging.DEBUG)
+    LOGGER.addHandler(console)
+
+import reciprocalspaceship as rs
+from reciprocalspaceship.decorators import cellify, spacegroupify
+from reciprocalspaceship.io.common import check_for_ray, set_ray_loglevel
+
+MSGPACK_DTYPES = {
+    "double": np.float64,
+    "float": np.float32,
+    "int": np.int32,
+    "cctbx::miller::index<>": np.int32,
+    "vec3<double>": np.float64,
+    "std::size_t": np.intp,
+}
+
+DEFAULT_COLS = [
+    "miller_index",
+    "intensity.sum.value",
+    "intensity.sum.variance",
+    "xyzcal.px",
+    "s1",
+    "delpsical.rad",
+    "id",
+]
+
+
+def _set_logger(verbose):
+    level = logging.CRITICAL
+    if verbose:
+        level = logging.DEBUG
+
+    for log_name in ("rs.io.dials", "ray"):
+        logger = logging.getLogger(log_name)
+        logger.setLevel(level)
+        for handler in logger.handlers:
+            handler.setLevel(level)
+
+
+def get_msgpack_data(data, name):
+    """
+
+    Parameters
+    ----------
+    data: msgpack data dict
+    name: msgpack data key
+
+    Returns
+    -------
+    numpy array of values
+    """
+    dtype, (num, buff) = data[name]
+    if dtype in MSGPACK_DTYPES:
+        dtype = MSGPACK_DTYPES[dtype]
+    else:
+        dtype = None  # should we warn here ?
+    vals = np.frombuffer(buff, dtype).reshape((num, -1))
+    data_dict = {}
+    for i, col_data in enumerate(vals.T):
+        data_dict[f"{name}.{i}"] = col_data
+
+    # remove the .0 suffix if data is a scalar type
+    if len(data_dict) == 1:
+        data_dict[name] = data_dict.pop(f"{name}.0")
+
+    return data_dict
+
+
+def _concat(refl_data):
+    """combine output of _get_refl_data"""
+    LOGGER.debug("Combining and formatting tables!")
+    if isinstance(refl_data, rs.DataSet):
+        ds = refl_data
+    else:
+        refl_data = [ds for ds in refl_data if ds is not None]
+        ds = rs.concat(refl_data, check_isomorphous=False)
+    expt_ids = set(ds.BATCH)
+    LOGGER.debug(f"Found {len(ds)} refls from {len(expt_ids)} expts.")
+    LOGGER.debug("Mapping batch column.")
+    expt_id_map = {name: i for i, name in enumerate(expt_ids)}
+    ds.BATCH = [expt_id_map[eid] for eid in ds.BATCH]
+    rename_map = {"miller_index.0": "H", "miller_index.1": "K", "miller_index.2": "L"}
+    ds.rename(columns=rename_map, inplace=True)
+    LOGGER.debug("Finished combining tables!")
+    return ds
+
+
+def _get_refl_data(fname, unitcell, spacegroup, extra_cols=None):
+    """
+
+    Parameters
+    ----------
+    fname: integrated refl file
+    unitcell: gemmi.UnitCell instance
+    spacegroup: gemmi.SpaceGroup instance
+    extra_cols: list of additional columns to read
+
+    Returns
+    -------
+    RS dataset (pandas Dataframe)
+
+    """
+    LOGGER.debug(f"Loading {fname}")
+    pack = _get_refl_pack(fname)
+    refl_data = pack["data"]
+    expt_id_map = pack["identifiers"]
+
+    if "miller_index" not in refl_data:
+        raise IOError("refl table must have a miller_index column")
+
+    ds_data = {}
+    col_names = DEFAULT_COLS if extra_cols is None else DEFAULT_COLS + extra_cols
+    for col_name in col_names:
+        if col_name in refl_data:
+            col_data = get_msgpack_data(refl_data, col_name)
+            LOGGER.debug(f"... Read in data for {col_name}")
+            ds_data = {**col_data, **ds_data}
+
+    if "id" in ds_data:
+        ds_data["BATCH"] = np.array([expt_id_map[li] for li in ds_data.pop("id")])
+    ds = rs.DataSet(
+        ds_data,
+        cell=unitcell,
+        spacegroup=spacegroup,
+    )
+    ds["PARTIAL"] = True
+    return ds
+
+
+def _read_dials_stills_serial(fnames, unitcell, spacegroup, extra_cols=None, **kwargs):
+    """run read_dials_stills without trying to import ray"""
+    result = [
+        _get_refl_data(fname, unitcell, spacegroup, extra_cols) for fname in fnames
+    ]
+    return result
+
+
+def _read_dials_stills_ray(fnames, unitcell, spacegroup, numjobs=10, extra_cols=None):
+    """
+
+    Parameters
+    ----------
+    fnames: integration files
+    unitcell: gemmi.UnitCell instance
+    spacegroup: gemmi.SpaceGroup instance
+    numjobs: number of jobs
+    extra_cols: list of additional columns to read from refl tables
+
+    Returns
+    -------
+    RS dataset (pandas Dataframe)
+    """
+    from reciprocalspaceship.io.common import ray_context
+
+    with ray_context(
+        log_level=LOGGER.level,
+        num_cpus=numjobs,
+        log_to_driver=LOGGER.level == logging.DEBUG,
+    ) as ray:
+        # get the refl data
+        get_refl_data = ray.remote(_get_refl_data)
+        refl_data = ray.get(
+            [
+                get_refl_data.remote(fname, unitcell, spacegroup, extra_cols)
+                for fname in fnames
+            ]
+        )
+    return refl_data
+
+
+def dials_to_mtz_dtypes(ds, inplace=True):
+    """
+    Coerce the dtypes in ds into ones that can be written to an mtz file.
+    This will downcast doubles to single precision. If "variance" columns
+    are present, they will be converted to "sigma" and assigned
+    StandardDeviationDtype.
+
+    Parameters
+    ----------
+    ds : rs.DataSet
+    inplace : bool (optional)
+        Convert ds dtypes in place without makeing a copy. Defaults to True.
+
+    Returns
+    -------
+    ds : rs.DataSet
+    """
+    rename_map = {}
+    for name in ds:
+        if "variance" in name:
+            new_name = name.replace("variance", "sigma")
+            rename_map[name] = new_name
+            ds[name] = np.sqrt(ds[name]).astype("Q")
+            LOGGER.debug(
+                f"Converted column {name} to MTZ-Type Q, took sqrt of the values, and renamed to {new_name}."
+            )
+    ds.rename(columns=rename_map, inplace=True)
+    ds.infer_mtz_dtypes(inplace=True)
+    return ds
+
+
+@cellify
+@spacegroupify
+def read_dials_stills(
+    fnames,
+    unitcell=None,
+    spacegroup=None,
+    numjobs=10,
+    parallel_backend=None,
+    extra_cols=None,
+    verbose=False,
+    comm=None,
+    mtz_dtypes=False,
+):
+    """
+    Read reflections from still images processed by DIALS from fnames and return
+    them as a DataSet. By default, this function will not convert the data from
+    dials into an MTZ compatible format.
+
+    Parameters
+    ----------
+    fnames : list or tuple or string
+        A list or tuple of filenames (strings) or a single filename.
+    unitcell : gemmi.UnitCell or similar (optional)
+        The unit cell assigned to the returned dataset.
+    spacegroup : gemmi.SpaceGroup or similar (optional)
+        The spacegroup assigned to the returned dataset.
+    numjobs : int
+        If backend==ray, specify the number of jobs (ignored if backend==mpi).
+    parallel_backend : string (optional)
+        "ray", "mpi", or None for serial.
+    extra_cols : list (optional)
+        Optional list of additional column names to extract from the refltables. By default, this method will search for
+        miller_index, id, s1, xyzcal.px, intensity.sum.value, intensity.sum.variance, delpsical.rad
+    verbose : bool
+        Whether to print logging info to stdout
+    comm : mpi4py.MPI.Comm
+        Optionally override the communicator used by backend='mpi'
+    mtz_dtypes : bool (optional)
+        Optionally convert columns to mtz compatible dtypes. Note this will downcast double precision (64-bit)
+        floats to single precision (32-bit).
+
+    Returns
+    -------
+    ds : rs.DataSet
+        The dataset containing reflection info aggregated from fnames. This method will not convert any of the
+        columns to native rs MTZ dtypes. DIALS data are natively double precision (64-bit). Converting to MTZ
+        will downcast them to 32-bit. Use ds.infer_mtz_dtypes() to convert to native rs dtypes if required.
+    """
+    _set_logger(verbose)
+    if isinstance(fnames, str):
+        fnames = [fnames]
+
+    if parallel_backend not in ["ray", "mpi", None]:
+        raise NotImplementedError("parallel_backend should be ray, mpi, or none")
+
+    kwargs = {
+        "fnames": fnames,
+        "unitcell": unitcell,
+        "spacegroup": spacegroup,
+        "extra_cols": extra_cols,
+    }
+    reader = _read_dials_stills_serial
+    if parallel_backend == "ray":
+        kwargs["numjobs"] = numjobs
+        from reciprocalspaceship.io.common import check_for_ray
+
+        if check_for_ray():
+            reader = _read_dials_stills_ray
+    elif parallel_backend == "mpi":
+        from reciprocalspaceship.io.common import check_for_mpi
+
+        if check_for_mpi():
+            from reciprocalspaceship.io.dials_mpi import read_dials_stills_mpi as reader
+
+            kwargs["comm"] = comm
+    result = reader(**kwargs)
+    if result is not None:
+        result = _concat(result)
+    if mtz_dtypes:
+        dials_to_mtz_dtypes(result, inplace=True)
+    return result
+
+
+def _get_refl_pack(filename):
+    pack = msgpack.load(open(filename, "rb"), strict_map_key=False)
+    try:
+        assert len(pack) == 3
+        _, _, pack = pack
+    except (TypeError, AssertionError):
+        raise IOError("File does not appear to be dials::af::reflection_table")
+    return pack
+
+
+def print_refl_info(reflfile):
+    """print contents of `fname`, a reflection table file saved with DIALS"""
+    pack = _get_refl_pack(reflfile)
+    if "identifiers" in pack:
+        idents = pack["identifiers"]
+        print(f"\nFound {len(idents)} experiment identifiers in {reflfile}:")
+        for i, ident in idents.items():
+            print(f"\t{i}: {ident}")
+    if "data" in pack:
+        data = pack["data"]
+        columns = []
+        col_space = 0
+        for name in data:
+            dtype, (_, buff) = data[name]
+            columns.append((name, dtype))
+            col_space = max(len(dtype), len(name), col_space)
+        names, dtypes = zip(*columns)
+        df = pandas.DataFrame({"names": names, "dtypes": dtypes})
+        print(
+            "\nReflection contents:\n"
+            + df.to_string(index=False, col_space=col_space + 5, justify="center")
+        )
+
+    if "nrows" in pack:
+        print(f"\nNumber of reflections: {pack['nrows']} \n")

reciprocalspaceship/io/dials_mpi.py

@@ -0,0 +1,44 @@
+from itertools import chain
+
+from reciprocalspaceship.decorators import cellify, spacegroupify
+from reciprocalspaceship.io import dials
+
+
+def mpi_starmap(comm, func, iterable):
+    results = []
+    for i, item in enumerate(iterable):
+        if i % comm.size == comm.rank:
+            results.append(func(*item))
+    results = comm.gather(results)
+    if comm.rank == 0:
+        return chain.from_iterable(results)
+    return None
+
+
+@cellify
+@spacegroupify
+def read_dials_stills_mpi(fnames, unitcell, spacegroup, extra_cols=None, comm=None):
+    """
+
+    Parameters
+    ----------
+    fnames: integrated reflection tables
+    unitcell: unit cell tuple (6 params Ang,Ang,Ang,deg,deg,deg)
+    spacegroup: space group name e.g. P4
+    extra_cols: list of additional column names to read from the refl table
+    comm: Optionally override the MPI communicator. The default is MPI.COMM_WORLD
+
+    Returns
+    -------
+    RS dataset (pandas Dataframe) if MPI rank==0 else None
+    """
+    if comm is None:
+        from mpi4py import MPI
+
+        comm = MPI.COMM_WORLD
+    ds = mpi_starmap(
+        comm,
+        dials._get_refl_data,
+        ((f, unitcell, spacegroup, extra_cols) for f in fnames),
+    )
+    return ds

reciprocalspaceship/io/mtz.py

@@ -133,16 +133,15 @@ def to_gemmi(
     mtz.datasets[0].dataset_name = dataset_name
 
     # Construct data for Mtz object
-    temp = dataset.reset_index()
+    # GH#255: DataSet is provided using the range_indexed decorator
     columns = []
-    for c in temp.columns:
-        cseries = temp[c]
+    for c in dataset.columns:
+        cseries = dataset[c]
         if isinstance(cseries.dtype, MTZDtype):
             mtz.add_column(label=c, type=cseries.dtype.mtztype)
             columns.append(c)
         # Special case for CENTRIC and PARTIAL flags
         elif cseries.dtype.name == "bool" and c in ["CENTRIC", "PARTIAL"]:
-            temp[c] = temp[c].astype("MTZInt")
             mtz.add_column(label=c, type="I")
             columns.append(c)
         elif skip_problem_mtztypes:
@@ -152,7 +151,7 @@ def to_gemmi(
                 f"column {c} of type {cseries.dtype} cannot be written to an MTZ file. "
                 f"To skip columns without explicit MTZ dtypes, set skip_problem_mtztypes=True"
             )
-    mtz.set_data(temp[columns].to_numpy(dtype="float32"))
+    mtz.set_data(dataset[columns].to_numpy(dtype="float32"))
 
     # Handle Unmerged data
     if not dataset.merged and not all_in_asu:

reciprocalspaceship/utils/__init__.py

@@ -52,4 +52,9 @@ from reciprocalspaceship.utils.symmetry import (
     phase_shift,
     polar_axes,
 )
-from reciprocalspaceship.utils.units import angstroms2ev, ev2angstroms
+from reciprocalspaceship.utils.units import (
+    Angstroms2eV,
+    angstroms2ev,
+    ev2angstroms,
+    eV2Angstroms,
+)

reciprocalspaceship/utils/cell.py

@@ -24,6 +24,11 @@ def compute_dHKL(H, cell):
     # Compress the hkls so we don't do redudant computation
     H = np.array(H, dtype=np.float32)
     hkls, inverse = np.unique(H, axis=0, return_inverse=True)
+
+    # The behavior of np.unique changed with v2.0. This block maintains v1 compatibility
+    if inverse.shape[-1] == 1:
+        inverse = inverse.squeeze(-1)
+
     F = np.array(cell.fractionalization_matrix.tolist()).astype(np.float64)
     dhkls = np.reciprocal(np.linalg.norm((hkls @ F), 2, 1)).astype(np.float32)
     return dhkls[inverse]

reciprocalspaceship/utils/stats.py

@@ -41,8 +41,6 @@ def compute_redundancy(
     if dmin is None:
         dmin = dhkl.min()
     hobs = hobs[dhkl >= dmin]
-    decimals = 5.0  # Round after this many decimals
-    dmin = np.floor(dmin * 10**decimals) * 10**-decimals
     hobs, isym = rs.utils.hkl_to_asu(hobs, spacegroup)
     if anomalous:
         fminus = isym % 2 == 0
@@ -107,15 +105,15 @@ def weighted_pearsonr(x, y, w):
     """
     z = np.reciprocal(w.sum(-1))
 
-    mx = z * (w * x).sum(-1)
-    my = z * (w * y).sum(-1)
+    mx = z * np.einsum("...a,...a->...", w, x)
+    my = z * np.einsum("...a,...a->...", w, y)
 
     dx = x - np.expand_dims(mx, axis=-1)
     dy = y - np.expand_dims(my, axis=-1)
 
-    cxy = z * (w * dx * dy).sum(-1)
-    cx = z * (w * dx * dx).sum(-1)
-    cy = z * (w * dy * dy).sum(-1)
+    cxy = z * np.einsum("...a,...a,...a->...", w, dx, dy)
+    cx = z * np.einsum("...a,...a,...a->...", w, dx, dx)
+    cy = z * np.einsum("...a,...a,...a->...", w, dy, dy)
 
     r = cxy / np.sqrt(cx * cy)
     return r

reciprocalspaceship/utils/structurefactors.py

@@ -104,6 +104,11 @@ def is_centric(H, spacegroup):
     """
     group_ops = spacegroup.operations()
     hkl, inverse = np.unique(H, axis=0, return_inverse=True)
+
+    # The behavior of np.unique changed with v2.0. This block maintains v1 compatibility
+    if inverse.shape[-1] == 1:
+        inverse = inverse.squeeze(-1)
+
     centric = group_ops.centric_flag_array(hkl)
     return centric[inverse]
 

reciprocalspaceship/utils/units.py

@@ -1,9 +1,19 @@
+import numpy as np
 from scipy.constants import Planck, c, electron_volt
 
+_conversion_factor = Planck * c / 1e-10 / electron_volt
 
-def ev2angstroms(ev):
-    return Planck * c / ev / 1e-10 / electron_volt
 
+def eV2Angstroms(ev):
+    out = np.empty_like(ev)
+    np.divide(_conversion_factor, ev, out=out)
+    return out
 
-def angstroms2ev(angstroms):
-    return Planck * c / angstroms / 1e-10 / electron_volt
+
+def Angstroms2eV(angstroms):
+    return eV2Angstroms(angstroms)
+
+
+# Add legacy aliases
+ev2angstroms = eV2Angstroms
+angstroms2ev = Angstroms2eV

{reciprocalspaceship-1.0.1.dist-info → reciprocalspaceship-1.0.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: reciprocalspaceship
-Version: 1.0.1
+Version: 1.0.3
 Summary: Tools for exploring reciprocal space
 Home-page: https://rs-station.github.io/reciprocalspaceship/
 Author: Kevin M. Dalton, Jack B. Greisman
@@ -9,7 +9,6 @@ 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
-Platform: UNKNOWN
 Classifier: Development Status :: 3 - Alpha
 Classifier: Intended Audience :: Developers
 Classifier: Intended Audience :: Science/Research
@@ -18,36 +17,38 @@ Classifier: Topic :: Scientific/Engineering :: Chemistry
 Classifier: Topic :: Scientific/Engineering :: Physics
 Classifier: Topic :: Software Development :: Libraries :: Python Modules
 Classifier: Programming Language :: Python
-Requires-Python: >3.7
+Requires-Python: >=3.9
 License-File: LICENSE
-Requires-Dist: gemmi <=0.6.2,>=0.5.5
-Requires-Dist: pandas <=2.0.3,>=1.4.0
+Requires-Dist: gemmi<=0.6.7,>=0.5.5
+Requires-Dist: pandas<=2.2.3,>=2.2.2
 Requires-Dist: numpy
 Requires-Dist: scipy
 Requires-Dist: ipython
+Requires-Dist: msgpack
 Provides-Extra: dev
-Requires-Dist: pytest ; extra == 'dev'
-Requires-Dist: pytest-cov ; extra == 'dev'
-Requires-Dist: pytest-xdist ; extra == 'dev'
-Requires-Dist: sphinx ; extra == 'dev'
-Requires-Dist: sphinx-rtd-theme ; extra == 'dev'
-Requires-Dist: nbsphinx ; extra == 'dev'
-Requires-Dist: sphinx-design ; extra == 'dev'
-Requires-Dist: sphinxcontrib-autoprogram ; extra == 'dev'
-Requires-Dist: autodocsumm ; extra == 'dev'
-Requires-Dist: jupyter ; extra == 'dev'
-Requires-Dist: tqdm ; extra == 'dev'
-Requires-Dist: matplotlib ; extra == 'dev'
-Requires-Dist: seaborn ; extra == 'dev'
-Requires-Dist: celluloid ; extra == 'dev'
-Requires-Dist: scikit-image ; extra == 'dev'
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+Requires-Dist: pytest-xdist; extra == "dev"
+Requires-Dist: ray; extra == "dev"
+Requires-Dist: sphinx; extra == "dev"
+Requires-Dist: sphinx-rtd-theme; extra == "dev"
+Requires-Dist: nbsphinx; extra == "dev"
+Requires-Dist: sphinx-design; extra == "dev"
+Requires-Dist: sphinxcontrib-autoprogram; extra == "dev"
+Requires-Dist: autodocsumm; extra == "dev"
+Requires-Dist: jupyter; extra == "dev"
+Requires-Dist: tqdm; extra == "dev"
+Requires-Dist: matplotlib; extra == "dev"
+Requires-Dist: seaborn; extra == "dev"
+Requires-Dist: celluloid; extra == "dev"
+Requires-Dist: scikit-image; extra == "dev"
 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'
+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"
 
 
 ``reciprocalspaceship`` provides a ``pandas``-style interface for
@@ -68,5 +69,3 @@ Features of this library include:
     use space groups, unit cell parameters, and crystallographic symmetry
     operations.
   - Support for reading and writing MTZ reflection files.
-
-

{reciprocalspaceship-1.0.1.dist-info → reciprocalspaceship-1.0.3.dist-info}/RECORD

@@ -1,58 +1,62 @@
-reciprocalspaceship/VERSION,sha256=ROFh5ElcrCz3hYBD6eZBjpV58N3ProJvmjcmIpaM4GY,6
-reciprocalspaceship/__init__.py,sha256=69LJFzMjF05nmlwROByI53LTwM37sgrgYAp5k1n6wCs,1842
+reciprocalspaceship/VERSION,sha256=9eXJU0UyhA_NRbsALmnthcYduidTRQ4mtEi33xSB4k0,6
+reciprocalspaceship/__init__.py,sha256=m6pXLI-HuXwefCfSE2Rs_2McqzuHw5W6yMBXEbceke8,2034
 reciprocalspaceship/concat.py,sha256=v2eg8-RBiNLYHkkPDeaozh3HvGCaFbmlC15FaeNJMgY,1695
 reciprocalspaceship/dataseries.py,sha256=ibU1bHMd8zORFxRtDswtvLh_n-miAyBqO0ghLmY29Js,6188
-reciprocalspaceship/dataset.py,sha256=g7sQ9eMD3XM2jQ6LkQcuUtzhp1qVPXpwcYph_uovWOA,56836
-reciprocalspaceship/decorators.py,sha256=pMdbyH6_VAPGz5K4rUVXQ2zsjvN_TbPaPaO930ANmi0,5592
+reciprocalspaceship/dataset.py,sha256=6GMIMWVdKzOFhFsgODgvFn2-hrrMRMPw3-oDzlbL0YQ,57698
+reciprocalspaceship/decorators.py,sha256=sZAPAV5fk5zUlwzub2VZy-u28XVNXjBpnqwnKjESWgY,5721
 reciprocalspaceship/algorithms/__init__.py,sha256=r5IYCGswTHXpSs9Q7c6PfEz8_P8d1fEei2SyTkp5aYY,258
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