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Merge pull request #13087 from jj-umn/neper_datatypes
Add Neper and Gmsh datatypes
This commit is contained in:
Marius van den Beek
@@ -886,6 +886,19 @@
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<datatype extension="npz" type="galaxy.datatypes.binary:Npz" display_in_upload="true"/>
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<datatype extension="hexrd.images.npz" type="galaxy.datatypes.binary:HexrdImagesNpz" display_in_upload="true"/>
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<datatype extension="hexrd.eta_ome.npz" type="galaxy.datatypes.binary:HexrdEtaOmeNpz" display_in_upload="true"/>
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<datatype extension="hexrd.scored_orientations.npz" type="galaxy.datatypes.binary:Npz" subclass="true" display_in_upload="true"/>
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<datatype extension="hexrd.accepted_orientations" type="galaxy.datatypes.tabular:Tabular" mimetype="application/text" subclass="true" display_in_upload="true" />
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<datatype extension="hexrd.yml" type="galaxy.datatypes.text:Yaml" subclass="true" display_in_upload="true"/>
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<datatype extension="neper.tess" type="galaxy.datatypes.constructive_solid_geometry:NeperTess" display_in_upload="true"/>
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<datatype extension="neper.tesr" type="galaxy.datatypes.constructive_solid_geometry:NeperTesr" display_in_upload="true"/>
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<datatype extension="neper.points" type="galaxy.datatypes.constructive_solid_geometry:NeperPoints" display_in_upload="true"/>
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<datatype extension="neper.points.tsv" type="galaxy.datatypes.constructive_solid_geometry:NeperPointsTabular" display_in_upload="true"/>
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<datatype extension="neper.mscell" type="galaxy.datatypes.constructive_solid_geometry:NeperMultiScaleCell" display_in_upload="true"/>
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<datatype extension="gmsh.msh" type="galaxy.datatypes.constructive_solid_geometry:GmshMsh" display_in_upload="true"/>
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<datatype extension="gmsh.geo" type="galaxy.datatypes.constructive_solid_geometry:GmshGeo" display_in_upload="true"/>
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<datatype extension="zset.geof" type="galaxy.datatypes.constructive_solid_geometry:ZsetGeof" display_in_upload="true"/>
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<!-- Povray script -->
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<datatype extension="pov" type="galaxy.datatypes.text:Text" subclass="true" display_in_upload="true"/>
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<!-- End Structural Materials datatypes -->
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</registration>
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<sniffers>
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@@ -915,6 +928,9 @@
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<sniffer type="galaxy.datatypes.constructive_solid_geometry:PlyBinary"/>
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<sniffer type="galaxy.datatypes.constructive_solid_geometry:VtkAscii"/>
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<sniffer type="galaxy.datatypes.constructive_solid_geometry:VtkBinary"/>
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<sniffer type="galaxy.datatypes.constructive_solid_geometry:NeperTess"/>
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<sniffer type="galaxy.datatypes.constructive_solid_geometry:NeperTesr"/>
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<sniffer type="galaxy.datatypes.constructive_solid_geometry:GmshMsh"/>
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<sniffer type="galaxy.datatypes.goldenpath:GoldenPath"/>
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<sniffer type="galaxy.datatypes.interval:ScIdx"/>
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<sniffer type="galaxy.datatypes.tabular:Vcf"/>
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@@ -17,6 +17,7 @@ from galaxy.datatypes.sniff import (
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build_sniff_from_prefix,
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FilePrefix,
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)
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from galaxy.datatypes.tabular import Tabular
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MAX_HEADER_LINES = 500
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MAX_LINE_LEN = 2000
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@@ -492,6 +493,277 @@ class STL(data.Data):
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file_ext = "stl"
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@build_sniff_from_prefix
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class NeperTess(data.Text):
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"""
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Neper Tessellation File
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***tess
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**format
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format
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**general
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dim type
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**cell
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number_of_cells
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"""
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file_ext = "neper.tess"
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MetadataElement(name="format", default=None, desc="format", readonly=True, visible=True, no_value=None)
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MetadataElement(name="dimension", default=None, desc="dimension", readonly=True, visible=True, no_value=None)
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MetadataElement(name="cells", default=None, desc="cells", readonly=True, visible=True, no_value=None)
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def __init__(self, **kwd):
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data.Text.__init__(self, **kwd)
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def sniff_prefix(self, file_prefix: FilePrefix):
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"""
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Neper tess format startswith:***tess
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>>> from galaxy.datatypes.sniff import get_test_fname
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>>> fname = get_test_fname('test.neper.tess')
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>>> NeperTess().sniff(fname)
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True
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>>> fname = get_test_fname('test.neper.tesr')
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>>> NeperTess().sniff(fname)
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False
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"""
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return file_prefix.text_io(errors='ignore').readline(10).startswith('***tess')
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def set_meta(self, dataset, **kwd):
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if dataset.has_data():
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with open(dataset.file_name, errors='ignore') as fh:
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for i, line in enumerate(fh):
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line = line.strip()
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if not line or i > 6:
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break
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if i == 0 and not line.startswith('***tess'):
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break
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if i == 2:
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dataset.metadata.format = line
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if i == 4:
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dataset.metadata.dimension = int(line.split()[0])
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if i == 6:
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dataset.metadata.cells = int(line)
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def set_peek(self, dataset):
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if not dataset.dataset.purged:
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dataset.peek = get_file_peek(dataset.file_name, LINE_COUNT=7)
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dataset.blurb = f'format: {str(dataset.metadata.format)} dim: {str(dataset.metadata.dimension)} cells: {str(dataset.metadata.cells)}'
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else:
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dataset.peek = 'File does not exist'
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dataset.blurb = 'File purged from disc'
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@build_sniff_from_prefix
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class NeperTesr(Binary):
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"""
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Neper Raster Tessellation File
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***tesr
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**format
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format
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**general
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dimension
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size_x size_y [size_z]
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voxsize_x voxsize_y [voxsize_z]
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[*origin
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origin_x origin_y [origin_z]]
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[*hasvoid has_void]
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[**cell
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number_of_cells
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"""
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file_ext = "neper.tesr"
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MetadataElement(name="format", default=None, desc="format", readonly=True, visible=True, no_value=None)
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MetadataElement(name="dimension", default=None, desc="dimension", readonly=True, visible=True, no_value=None)
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MetadataElement(name="size", default=[], desc="size", readonly=True, visible=True, no_value=None)
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MetadataElement(name="voxsize", default=[], desc="voxsize", readonly=True, visible=True, no_value=None)
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MetadataElement(name="origin", default=[], desc="origin", readonly=True, visible=True, no_value=None)
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MetadataElement(name="cells", default=None, desc="cells", readonly=True, visible=True, no_value=None)
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def __init__(self, **kwd):
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Binary.__init__(self, **kwd)
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def sniff_prefix(self, file_prefix: FilePrefix):
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"""
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Neper tesr format startswith:***tesr
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>>> from galaxy.datatypes.sniff import get_test_fname
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>>> fname = get_test_fname('test.neper.tesr')
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>>> NeperTesr().sniff(fname)
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True
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>>> fname = get_test_fname('test.neper.tess')
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>>> NeperTesr().sniff(fname)
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False
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"""
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return file_prefix.text_io(errors='ignore').readline(10).startswith('***tesr')
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def set_meta(self, dataset, **kwd):
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if dataset.has_data():
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with open(dataset.file_name, errors='ignore') as fh:
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field = ''
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for i, line in enumerate(fh):
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line = line.strip()
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if not line or i > 12:
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break
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if i == 0 and not line.startswith('***tesr'):
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break
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if line.startswith('*'):
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field = line
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continue
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if i == 2:
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dataset.metadata.format = line.split()[0]
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continue
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if i == 4:
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dataset.metadata.dimension = line.split()[0]
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continue
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if i == 5:
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dataset.metadata.size = line.split()
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continue
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if i == 6:
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dataset.metadata.voxsize = line.split()
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continue
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if field.startswith('*origin'):
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dataset.metadata.origin = line.split()
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continue
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if field.startswith('**cell'):
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dataset.metadata.cells = int(line)
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break
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def set_peek(self, dataset):
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if not dataset.dataset.purged:
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dataset.peek = get_file_peek(dataset.file_name, LINE_COUNT=9)
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dataset.blurb = f'format: {str(dataset.metadata.format)} dim: {str(dataset.metadata.dimension)} cells: {str(dataset.metadata.cells)}'
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else:
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dataset.peek = 'File does not exist'
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dataset.blurb = 'File purged from disc'
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class NeperPoints(data.Text):
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"""
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Neper Position File
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Neper position format has 1 - 3 floats per line separated by white space.
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"""
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file_ext = "neper.points"
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MetadataElement(name="dimension", default=None, desc="dimension", readonly=True, visible=True, no_value=None)
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def __init__(self, **kwd):
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data.Text.__init__(self, **kwd)
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def set_meta(self, dataset, **kwd):
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data.Text.set_meta(self, dataset, **kwd)
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if dataset.has_data():
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with open(dataset.file_name, errors='ignore') as fh:
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dataset.metadata.dimension = self._get_dimension(fh)
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def _get_dimension(self, fh, maxlines=100, sep=None):
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dim = None
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try:
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for i, line in enumerate(fh):
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if not line:
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break
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pts = len([float(x) for x in line.strip().split(sep=sep)])
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if dim is not None and pts != dim:
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return None
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elif 1 <= pts <= 3:
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dim = pts
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else:
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return None
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if i > maxlines:
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break
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except Exception:
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return None
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return dim
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def set_peek(self, dataset):
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data.Text.set_peek(self, dataset)
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if not dataset.dataset.purged:
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dataset.blurb += f' dim: {str(dataset.metadata.dimension)}'
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class NeperPointsTabular(NeperPoints, Tabular):
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"""
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Neper Position File
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Neper position format has 1 - 3 floats per line separated by TABs.
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"""
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file_ext = "neper.points.tsv"
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def __init__(self, **kwd):
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Tabular.__init__(self, **kwd)
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def set_meta(self, dataset, **kwd):
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Tabular.set_meta(self, dataset, **kwd)
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if dataset.has_data():
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with open(dataset.file_name, errors='ignore') as fh:
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dataset.metadata.dimension = self._get_dimension(fh)
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def set_peek(self, dataset):
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Tabular.set_peek(self, dataset)
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if not dataset.dataset.purged:
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dataset.blurb += f' dim: {str(dataset.metadata.dimension)}'
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class NeperMultiScaleCell(data.Text):
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"""
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Neper Multiscale Cell File
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"""
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file_ext = "neper.mscell"
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@build_sniff_from_prefix
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class GmshMsh(Binary):
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"""Gmsh Mesh File"""
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file_ext = "gmsh.msh"
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MetadataElement(name="version", default=None, desc="version", readonly=True, visible=True, no_value=None)
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MetadataElement(name="format", default=None, desc="format", readonly=True, visible=True, no_value=None)
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def __init__(self, **kwd):
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Binary.__init__(self, **kwd)
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def sniff_prefix(self, file_prefix: FilePrefix):
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"""
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Gmsh msh format startswith:$MeshFormat
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>>> from galaxy.datatypes.sniff import get_test_fname
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>>> fname = get_test_fname('test.gmsh.msh')
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>>> GmshMsh().sniff(fname)
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True
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>>> fname = get_test_fname('test.neper.tesr')
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>>> GmshMsh().sniff(fname)
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False
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"""
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return file_prefix.text_io(errors='ignore').readline().startswith('$MeshFormat')
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def set_meta(self, dataset, **kwd):
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if dataset.has_data():
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with open(dataset.file_name, errors='ignore') as fh:
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for i, line in enumerate(fh):
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line = line.strip()
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if not line or i > 1:
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break
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if i == 0 and not line.startswith('$MeshFormat'):
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break
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if i == 1:
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fields = line.split()
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if len(fields) > 0:
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dataset.metadata.version = fields[0]
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if len(fields) > 1:
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dataset.metadata.format = 'ASCII' if fields[1] == '0' else 'binary'
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def set_peek(self, dataset):
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if not dataset.dataset.purged:
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dataset.peek = get_file_peek(dataset.file_name, LINE_COUNT=3)
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dataset.blurb = f'Gmsh verion: {str(dataset.metadata.version)} {str(dataset.metadata.format)}'
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else:
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dataset.peek = 'File does not exist'
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dataset.blurb = 'File purged from disc'
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class GmshGeo(data.Text):
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"""Gmsh geometry File"""
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file_ext = "gmsh.geo"
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class ZsetGeof(data.Text):
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"""
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Z-set geof File
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"""
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file_ext = "zset.geof"
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# Utility functions
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def get_next_line(fh):
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line = fh.readline(MAX_LINE_LEN)
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|
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File diff suppressed because it is too large
Load Diff
Binary file not shown.
@@ -0,0 +1,554 @@
|
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***tess
|
||||
**format
|
||||
3.4
|
||||
**general
|
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3 standard
|
||||
**cell
|
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10
|
||||
*id
|
||||
1 2 3 4 5 6 7 8 9 10
|
||||
*mode
|
||||
1 1 1 1 1 1 1 1 1 1
|
||||
*crysym
|
||||
triclinic
|
||||
*seed
|
||||
1 0.327544505352 0.059994859404 0.520245461924 0.000000000000
|
||||
2 0.463746603421 0.352810469826 0.017266972293 0.000000000000
|
||||
3 0.140016493288 0.914894611083 0.371457357317 0.000000000000
|
||||
4 0.348110723967 0.898568807683 0.620980766206 0.000000000000
|
||||
5 0.228136020208 0.772531206470 0.776879102353 0.000000000000
|
||||
6 0.747908502360 0.481969104081 0.987303741555 0.000000000000
|
||||
7 0.064469931529 0.184636624118 0.753216233629 0.000000000000
|
||||
8 0.799042535648 0.691676427394 0.041937630353 0.000000000000
|
||||
9 0.979422516210 0.597123611043 0.274389313947 0.000000000000
|
||||
10 0.621418434654 0.502629860059 0.490413780382 0.000000000000
|
||||
*ori
|
||||
rodrigues:active
|
||||
0.919953402851 1.412193625247 -0.358468593221
|
||||
-1.381019825878 0.030115972514 -3.318384436434
|
||||
0.540501980937 -0.787561454202 -0.735523888182
|
||||
-2.005448934444 0.199749071961 -1.999283218069
|
||||
5.163148738562 14.893183177083 5.316486583072
|
||||
1.919036671923 -0.744035465279 0.303477757891
|
||||
-0.581246451853 -2.835847764762 0.780360761158
|
||||
-2.211174665124 0.445317073444 0.934247527182
|
||||
-2.194677973955 -0.312638828364 -0.439479476190
|
||||
1.153229166270 -1.695620636026 0.825414393959
|
||||
**vertex
|
||||
54
|
||||
1 0.000000000000 0.000000000000 0.480836332398 0
|
||||
2 0.459755416589 0.000000000000 1.000000000000 0
|
||||
3 0.000000000000 0.000000000000 0.041458869036 0
|
||||
4 0.000000000000 0.393293813046 0.270420087688 0
|
||||
5 0.875164741475 0.000000000000 0.278445691339 0
|
||||
6 0.913900420561 0.000000000000 0.660033507666 0
|
||||
7 0.434151598161 0.327663532237 0.795784363147 0
|
||||
8 0.484257319426 0.051714829787 1.000000000000 0
|
||||
9 0.536170248205 0.000000000000 1.000000000000 0
|
||||
10 0.178728872392 0.472579545895 0.429825098041 0
|
||||
11 0.186998765476 0.462472809438 0.361331160813 0
|
||||
12 0.029093767212 0.415649197792 0.291312905140 0
|
||||
13 0.000000000000 0.000000000000 0.000000000000 0
|
||||
14 1.000000000000 0.000000000000 0.000000000000 0
|
||||
15 1.000000000000 0.040784654316 0.000000000000 0
|
||||
16 1.000000000000 0.000000000000 0.038752863502 0
|
||||
17 0.881546611618 0.000000000000 0.276318991687 0
|
||||
18 0.722421690362 0.420035938944 0.196343791871 0
|
||||
19 0.893965115199 0.264594293597 0.000000000000 0
|
||||
20 0.000000000000 0.582459991209 0.000000000000 0
|
||||
21 0.434001108634 0.704989536248 0.202228280672 0
|
||||
22 0.362001661576 0.790953398456 0.000000000000 0
|
||||
23 0.000000000000 0.409696248986 0.274168254683 0
|
||||
24 0.000000000000 1.000000000000 0.000000000000 0
|
||||
25 0.000000000000 1.000000000000 0.669057750529 0
|
||||
26 0.059688233947 1.000000000000 0.656084349367 0
|
||||
27 0.257144028346 0.573870922957 0.463532029818 0
|
||||
28 0.554516962647 1.000000000000 0.243413634122 0
|
||||
29 0.432807668780 1.000000000000 0.000000000000 0
|
||||
30 0.503947601476 0.807076535216 0.272964215305 0
|
||||
31 0.000000000000 0.529822736073 0.503955515921 0
|
||||
32 0.181969901270 0.481439284558 0.447414063030 0
|
||||
33 0.506581420832 1.000000000000 1.000000000000 0
|
||||
34 0.691298725730 1.000000000000 1.000000000000 0
|
||||
35 0.557938786910 0.677531596182 0.778820222491 0
|
||||
36 0.599315620615 0.911726674895 1.000000000000 0
|
||||
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|
||||
3 81 92 101
|
||||
8 2 3 2
|
||||
x1z0
|
||||
3 23 94 100
|
||||
9 2 5 8
|
||||
y0z1
|
||||
3 8 82 91
|
||||
10 2 2 1
|
||||
y0z0
|
||||
1 26
|
||||
11 2 4 3
|
||||
y1z0
|
||||
2 45 96
|
||||
12 2 7 6
|
||||
y1z1
|
||||
3 55 71 84
|
||||
*face
|
||||
6
|
||||
1 4 4 6 5 1
|
||||
4 1 2 3 4
|
||||
plane
|
||||
4 0.000000000000 1.000000000000 0.000000000000 0.000000000000
|
||||
x0
|
||||
5 1 9 18 33 46
|
||||
2 4 2 8 7 3
|
||||
4 5 6 7 8
|
||||
plane
|
||||
4 -1.000000000000 -1.000000000000 -0.000000000000 -0.000000000000
|
||||
x1
|
||||
5 10 39 50 55 60
|
||||
3 4 1 5 8 2
|
||||
4 3 9 5 10
|
||||
plane
|
||||
4 0.000000000000 0.000000000000 1.000000000000 0.000000000000
|
||||
y0
|
||||
6 2 11 40 47 56 61
|
||||
4 4 4 3 7 6
|
||||
4 11 7 12 1
|
||||
plane
|
||||
4 -1.000000000000 -0.000000000000 -1.000000000000 -0.000000000000
|
||||
y1
|
||||
6 19 26 34 41 51 57
|
||||
5 4 1 2 3 4
|
||||
4 10 8 11 4
|
||||
plane
|
||||
4 0.000000000000 0.000000000000 0.000000000000 1.000000000000
|
||||
z0
|
||||
4 12 20 52 58
|
||||
6 4 5 6 7 8
|
||||
4 2 12 6 9
|
||||
plane
|
||||
4 -1.000000000000 -0.000000000000 -0.000000000000 -1.000000000000
|
||||
z1
|
||||
5 3 27 35 42 48
|
||||
***end
|
||||
Reference in New Issue
Block a user