changeset 1:6e5e9abb4139 draft default tip

"planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hedm_lattice_parameter_correction commit a8f7424061c14ed403820ebddcda94a38006c699"

--- a/hedm_lattice_parameter_correction.xml	Thu May 19 16:48:22 2022 +0000
+++ b/hedm_lattice_parameter_correction.xml	Thu May 19 17:38:53 2022 +0000
@@ -10,7 +10,6 @@
         cp '$material' '$material_file' &&
         #set $instrument_file = $ln_name($instrument,'yml')
         cp '$instrument' '$instrument_file' &&
-        ls -ltr &&
         $__tool_directory__/lattice_parameter_correction.py
         --min-completeness $min_completeness
         $force_symmetry
@@ -18,7 +17,6 @@
         $grains
         --average_lattice '$lattice_out'
         --materials_out '$materials_out'
-        && ls -ltr
     ]]></command>
     <configfiles>
         <configfile name="hexrd_cfg"><![CDATA[#slurp

--- a/lattice_parameter_correction.py.orig	Thu May 19 16:48:22 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,121 +0,0 @@
-#!/usr/bin/env python3
-
-import argparse
-
-import numpy as np
-
-from hexrd import rotations as rot
-from hexrd import matrixutil as mutil
-from hexrd import config
-
-
-def _lp_calc(v_mat, f_mat, r_mat):
-    """
-    do strained lappi
-
-    Parameters
-    ----------
-    vmat : TYPE
-        DESCRIPTION.
-    f_mat : TYPE
-        DESCRIPTION.
-    r_mat : TYPE
-        DESCRIPTION.
-
-    Returns
-    -------
-    lparams : TYPE
-        DESCRIPTION.
-
-    """
-    f_prime = np.dot(v_mat, np.dot(r_mat, f_mat))
-    f_prime_hat = mutil.unitVector(f_prime)
-
-    lp_mags = mutil.columnNorm(f_prime)
-
-    lp_angs = np.hstack(
-        [np.arccos(np.dot(f_prime_hat[:, 1], f_prime_hat[:, 2])),
-         np.arccos(np.dot(f_prime_hat[:, 2], f_prime_hat[:, 0])),
-         np.arccos(np.dot(f_prime_hat[:, 0], f_prime_hat[:, 1]))]
-    )
-    return np.hstack([lp_mags, np.degrees(lp_angs)])
-
-
-def extract_lattice_parameters(
-        cfg_file, grains_file,
-        min_completeness=0.90, force_symmetry=False
-        ):
-    """
-    """
-    cfg = config.open(cfg_file)[0]
-
-    pd = cfg.material.plane_data
-    qsym_mats = rot.quatProductMatrix(pd.getQSym())
-
-    f_mat = pd.latVecOps['F']
-
-    gt = np.loadtxt(grains_file)
-
-    idx = gt[:, 1] >= min_completeness
-
-    expMaps = gt[idx, 3:6].T
-    vinv = gt[idx, 9:15]
-
-    lparms = []
-    for i in range(sum(idx)):
-        quat = rot.quatOfExpMap(expMaps[:, i].reshape(3, 1))
-        v_mat = np.linalg.inv(mutil.vecMVToSymm(vinv[i, :].reshape(6, 1)))
-        if force_symmetry:
-            for qpm in qsym_mats:
-                lparms.append(
-                    _lp_calc(v_mat, f_mat, rot.rotMatOfQuat(np.dot(qpm, quat)))
-                )
-        else:
-            lparms.append(
-                    _lp_calc(v_mat, f_mat, rot.rotMatOfQuat(quat))
-                )
-    lp_avg = np.average(np.vstack(lparms), axis=0)
-    return lp_avg, sum(idx), len(idx)
-
-
-if __name__ == '__main__':
-    """
-    maybe make this smart enough to average properly for symmetry?
-    """
-    parser = argparse.ArgumentParser(
-        description="Extract average lattice parameters from grains.out"
-    )
-    parser.add_argument(
-        'cfg', help="ff-HEDM config YAML file", type=str
-        )
-    parser.add_argument(
-        'grains_file', help="grains.out file", type=str
-    )
-    parser.add_argument(
-        '-m', '--min-completeness', help="completeness threshold", type=float,
-        default=0.75
-    )
-
-    parser.add_argument(
-        '-f', '--force-symmetry',
-        help="symmetrize results",
-        action="store_true"
-    )
-
-    args = parser.parse_args()
-
-    cfg_file = args.cfg
-    grains_file = args.grains_file
-    min_completeness = args.min_completeness
-    force_symmetry = args.force_symmetry
-
-    lp_avg, n_used, n_total = extract_lattice_parameters(
-        cfg_file, grains_file,
-        min_completeness=min_completeness, force_symmetry=force_symmetry
-    )
-    print("Using %d grains out of %d above %.2f%% completeness threshold:"
-          % (n_used, n_total, 100*min_completeness))
-    print("---------------------------------------------------------------")
-    print("a       \tb       \tc       "
-          + "\talpha   \tbeta    \tgamma \n"
-          + "%.6f\t%.6f\t%.6f\t%.6f\t%.6f\t%.6f" % tuple(lp_avg))