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add hexrd_materials tool #10

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add hexrd_materials tool #10

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3 changes: 2 additions & 1 deletion tools/hexrd/datatypes_conf.xml
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Expand Up @@ -2,7 +2,8 @@
<datatypes>
<registration>
<datatype extension="hexrd.materials.h5" type="galaxy.datatypes.binary:H5" subclass="true" display_in_upload="true"/>
<datatype extension="hexrd.npz" type="galaxy.datatypes.binary:CompressedZipArchive" subclass="true" display_in_upload="true"/>
<datatype extension="hexrd.images.npz" type="galaxy.datatypes.binary:CompressedZipArchive" subclass="true" display_in_upload="true"/>
<datatype extension="hexrd.eta_ome.npz" type="galaxy.datatypes.binary:CompressedZipArchive" subclass="true" display_in_upload="true"/>
<datatype extension="hexrd.yml" type="galaxy.datatypes.data:Text" subclass="true" display_in_upload="true"/>
</registration>
</datatypes>
155 changes: 155 additions & 0 deletions tools/hexrd/hexrd_materials.xml
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<tool id="hexrd_materials" name="Make HEXRD Materials file" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5">
<description>Add or edit materials</description>
<macros>
<import>macros.xml</import>
<xml name="add_material">
<repeat name="add_materials" title="Add material">
<param name="material_name" type="text" value="" label="Name for material">
<yield/>
<validator type="empty_field" />
</param>
<param name="min_d_spacing" type="float" value="0.75" min=".1" label="Min d-spacing in Angstroms"/>
<expand macro="lattice"/>
</repeat>
</xml>
<xml name="space_group" token_ltype="triclinic">
<param name="space_group" type="select" label="Select Space Group">
<options from_data_table="hexrd_space_groups">
<column name="value" index="0"/>
<column name="name" index="1"/>
<filter type="static_value" name="ltype" value="@LTYPE@" column="2"/>
</options>
</param>
</xml>
<xml name="cell_a" token_val="" token_min="" token_max="">
<param name="cell_a" type="float" value="@VAL@" min="@MIN@" max="@MAX@" label="latitice cell a"/>
</xml>
<xml name="cell_b" token_val="" token_min="" token_max="">
<param name="cell_b" type="float" value="@VAL@" min="@MIN@" max="@MAX@" label="latitice cell b"/>
</xml>
<xml name="cell_c" token_val="" token_min="" token_max="">
<param name="cell_c" type="float" value="@VAL@" min="@MIN@" max="@MAX@" label="latitice cell c"/>
</xml>
<xml name="cell_alpha" token_val="90" token_min="90" token_max="90">
<param name="cell_alpha" type="float" value="@VAL@" min="@MIN@" max="@MAX@" label="latitice cell alpha"/>
</xml>
<xml name="cell_beta" token_val="90" token_min="90" token_max="90">
<param name="cell_beta" type="float" value="@VAL@" min="@MIN@" max="@MAX@" label="latitice cell beta"/>
</xml>
<xml name="cell_gamma" token_val="90" token_min="90" token_max="90">
<param name="cell_gamma" type="float" value="@VAL@" min="@MIN@" max="@MAX@" label="latitice cell gamma"/>
</xml>
<xml name="lattice">
<conditional name="lattice">
<param name="lattice_type" type="select" label="SpaceGroup lattice type">
<option value="triclinic">triclinic - SpaceGroups: 1 - 2</option>
<option value="monoclinic">monoclinic - SpaceGroups: 3 - 15</option>
<option value="orthorhombic">orthorhombic - SpaceGroups: 16 - 74</option>
<option value="tetragonal">tetragonal - SpaceGroups: 75 - 142</option>
<option value="trigonal">trigonal - SpaceGroups: 143 - 167</option>
<option value="hexagonal">hexagonal - SpaceGroups: 168 - 194</option>
<option value="cubic">cubic - SpaceGroups: 195 - 230</option>
</param>
<when value="triclinic">
<expand macro="space_group" ltype="triclinic"/>
<expand macro="cell_a" val="5" min="1.0" max="10.0"/>
<expand macro="cell_b" val="5" min="1.0" max="10.0"/>
<expand macro="cell_c" val="5" min="1.0" max="10.0"/>
<expand macro="cell_alpha" val="90" min="30.0" max="180.0"/>
<expand macro="cell_beta" val="90" min="30.0" max="180.0"/>
<expand macro="cell_gamma" val="90" min="30.0" max="180.0"/>
</when>
<when value="monoclinic">
<expand macro="space_group" ltype="monoclinic"/>
<expand macro="cell_a" val="5" min="1.0" max="10.0"/>
<expand macro="cell_b" val="5" min="1.0" max="10.0"/>
<expand macro="cell_c" val="5" min="1.0" max="10.0"/>
<param name="cell_alpha" type="hidden" value="90.0"/>
<expand macro="cell_beta" val="90.0" min="30.0" max="180.0"/>
<param name="cell_gamma" type="hidden" value="90.0"/>
</when>
<when value="orthorhombic">
<expand macro="space_group" ltype="orthorhombic"/>
<expand macro="cell_a" val="5" min="1.0" max="10.0"/>
<expand macro="cell_b" val="5" min="1.0" max="10.0"/>
<expand macro="cell_c" val="5" min="1.0" max="10.0"/>
<param name="cell_alpha" type="hidden" value="90.0"/>
<param name="cell_beta" type="hidden" value="90.0"/>
<param name="cell_gamma" type="hidden" value="90.0"/>
</when>
<when value="tetragonal">
<expand macro="space_group" ltype="tetragonal"/>
<expand macro="cell_a" val="5" min="1.0" max="10.0"/>
<expand macro="cell_c" val="5" min="1.0" max="10.0"/>
</when>
<when value="trigonal">
<expand macro="space_group" ltype="trigonal"/>
<expand macro="cell_a" val="5" min="1.0" max="10.0"/>
<expand macro="cell_c" val="5" min="1.0" max="10.0"/>
</when>
<when value="hexagonal">
<expand macro="space_group" ltype="hexagonal"/>
<expand macro="cell_a" val="5" min="1.0" max="10.0"/>
<expand macro="cell_c" val="5" min="1.0" max="10.0"/>
</when>
<when value="cubic">
<expand macro="space_group" ltype="cubic"/>
<expand macro="cell_a" val="5" min="1.0" max="10.0"/>
</when>
</conditional>
</xml>
</macros>
<expand macro="requirements" />
<command detect_errors="exit_code"><![CDATA[
#if $materials.file == 'modify':
ln -s '$materials.input' materials.h5 &&
#end if
python $__tool_directory__/make_materials.py
#if $materials.file == 'modify':
-i materials.h5
#end if
#for $mat in $materials.add_materials:
#if $mat.lattice.lattice_type == 'triclinic'
-m '$mat.material_name,$mat.lattice.space_group,$mat.lattice.cell_a,$mat.lattice.cell_b,$mat.lattice.cell_c,$mat.lattice.cell_alpha,$mat.lattice.cell_beta,$mat.lattice.cell_gamma'
#elif $mat.lattice.lattice_type == 'monoclinic':
-m '$mat.material_name,$mat.lattice.space_group,$mat.lattice.cell_a,$mat.lattice.cell_b,$mat.lattice.cell_c,$mat.lattice.cell_beta'
#elif $mat.lattice.lattice_type == 'orthorhombic':
-m '$mat.material_name,$mat.lattice.space_group,$mat.lattice.cell_a,$mat.lattice.cell_b,$mat.lattice.cell_c'
#elif $mat.lattice.lattice_type == 'tetragonal':
-m '$mat.material_name,$mat.lattice.space_group,$mat.lattice.cell_a,$mat.lattice.cell_c'
#elif $mat.lattice.lattice_type == 'trigonal':
-m '$mat.material_name,$mat.lattice.space_group,$mat.lattice.cell_a,$mat.lattice.cell_c'
#elif $mat.lattice.lattice_type == 'hexagonal':
-m '$mat.material_name,$mat.lattice.space_group,$mat.lattice.cell_a,$mat.lattice.cell_c'
#elif $mat.lattice.lattice_type == 'cubic':
-m '$mat.material_name,$mat.lattice.space_group,$mat.lattice.cell_a'
#end if
#end for
-o '$output'
]]></command>
<inputs>
<conditional name="materials">
<param name="file" type="select" label="Make HEXRD materials file">
<option value="modify">Modify an existing materials file</option>
<option value="create">Create new materials file</option>
</param>
<when value="modify">
<param name="input" type="data" format="hexrd.materials.h5" label="Edit existing materials file"/>
<expand macro="add_material">
<options>
<filter type="data_meta" ref="input" key="materials" />
</options>
</expand>
</when>
<when value="create">
<expand macro="add_material"/>
</when>
</conditional>
</inputs>
<outputs>
<data name="output" format="hexrd.materials.h5" label="Materials file"/>
</outputs>
<help><![CDATA[
TODO: Fill in help.
]]></help>
</tool>
72 changes: 72 additions & 0 deletions tools/hexrd/make_materials.py
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#!/usr/bin/env python

import argparse
import pathlib

from hexrd.material import load_materials_hdf5, save_materials_hdf5, Material
import numpy as np


def make_matl(mat_name, sgnum, lparms, hkl_ssq_max=50):
matl = Material(mat_name)
matl.name = mat_name
matl.sgnum = sgnum
matl.latticeParameters = lparms
matl.hklMax = hkl_ssq_max
nhkls = len(matl.planeData.exclusions)
matl.planeData.set_exclusions(np.zeros(nhkls, dtype=bool))
return matl


def __main__():
parser = argparse.ArgumentParser(description='', epilog='')
parser.add_argument('-i', '--input',
type=pathlib.Path,
nargs='?', default=None,
help='A materials file to edit')
parser.add_argument('-c', '--cif',
type=pathlib.Path,
## nargs='*',
default=[], action='append',
help='material.cif file')
parser.add_argument('-o', '--output',
type=pathlib.Path,
default='materials.h5',
help='Materials output file')
parser.add_argument('-m', '--material',
## nargs='*',
default=[], action='append',
help='Material ')
args = parser.parse_args()

materials = {}
if args.input:
materials = load_materials_hdf5(args.input)
for i, cifpath in enumerate(args.cif):
cif = str(cifpath.resolve())
print(cif)
try:
name = 'cif_' + str(i)
mat = Material(name, material_file=cif)
## print(mat)
materials[name] = mat
except Exception as e:
print(cif, e)
for mat in args.material:
print(mat)
try:
fields = [x.strip() for x in mat.split(',')]
# ftypes = (str, int, float, float, float, float, float, float)
# (name, spacegroup, a, b, c, alpha, beta, gamma) = [t(s) for t, s in zip(ftypes, fields[0:8])]
name = str(fields[0])
spacegroup = int(fields[1])
lattice_params = [float(x) for x in fields[2:]]
materials[name] = make_matl(name, spacegroup, lattice_params)
except Exception as e:
print(mat, e)
print(materials.keys())
save_materials_hdf5(args.output, materials)


if __name__ == "__main__":
__main__()
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