Merge remote-tracking branch 'origin/development' into polishing
This commit is contained in:
Martin Diehl
commit
c2453c56f1
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@ -1 +1 @@
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v3.0.0-alpha6-71-g3bc1a5eda
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v3.0.0-alpha6-88-g2162442e0
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@ -34,7 +34,8 @@ class Grid:
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material: np.ndarray,
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material: np.ndarray,
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size: FloatSequence,
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size: FloatSequence,
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origin: FloatSequence = np.zeros(3),
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origin: FloatSequence = np.zeros(3),
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comments: Union[str, Sequence[str]] = None):
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comments: Union[str, Sequence[str]] = None,
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initial_conditions = None):
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"""
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"""
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New geometry definition for grid solvers.
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New geometry definition for grid solvers.
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@ -55,10 +56,10 @@ class Grid:
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self.size = size # type: ignore
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self.size = size # type: ignore
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self.origin = origin # type: ignore
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self.origin = origin # type: ignore
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self.comments = [] if comments is None else comments # type: ignore
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self.comments = [] if comments is None else comments # type: ignore
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self.ic = initial_conditions if initial_conditions is not None else {}
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def __repr__(self) -> str:
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def __repr__(self) -> str:
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"""Basic information on grid definition."""
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"""Give short human-readable summary."""
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mat_min = np.nanmin(self.material)
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mat_min = np.nanmin(self.material)
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mat_max = np.nanmax(self.material)
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mat_max = np.nanmax(self.material)
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mat_N = self.N_materials
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mat_N = self.N_materials
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@ -68,7 +69,7 @@ class Grid:
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f'origin: {util.srepr(self.origin," ")} m',
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f'origin: {util.srepr(self.origin," ")} m',
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f'# materials: {mat_N}' + ('' if mat_min == 0 and mat_max+1 == mat_N else
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f'# materials: {mat_N}' + ('' if mat_min == 0 and mat_max+1 == mat_N else
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f' (min: {mat_min}, max: {mat_max})')
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f' (min: {mat_min}, max: {mat_max})')
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])
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]+(['initial_conditions:']+[f' - {f}' for f in self.ic.keys()] if self.ic else []))
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def __copy__(self) -> 'Grid':
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def __copy__(self) -> 'Grid':
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@ -187,11 +188,13 @@ class Grid:
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cells = np.array(v.vtk_data.GetDimensions())-1
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cells = np.array(v.vtk_data.GetDimensions())-1
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bbox = np.array(v.vtk_data.GetBounds()).reshape(3,2).T
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bbox = np.array(v.vtk_data.GetBounds()).reshape(3,2).T
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comments = v.comments
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comments = v.comments
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ic = {label:v.get(label).reshape(cells,order='F') for label in set(v.labels['Cell Data']) - {'material'}}
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return Grid(material = v.get('material').reshape(cells,order='F'),
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return Grid(material = v.get('material').reshape(cells,order='F'),
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size = bbox[1] - bbox[0],
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size = bbox[1] - bbox[0],
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origin = bbox[0],
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origin = bbox[0],
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comments=comments)
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comments = comments,
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initial_conditions = ic)
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@typing. no_type_check
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@typing. no_type_check
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@ -660,6 +663,8 @@ class Grid:
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"""
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"""
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v = VTK.from_image_data(self.cells,self.size,self.origin)\
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v = VTK.from_image_data(self.cells,self.size,self.origin)\
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.add(self.material.flatten(order='F'),'material')
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.add(self.material.flatten(order='F'),'material')
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for label,data in self.ic.items():
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v = v.add(data.flatten(order='F'),label)
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v.comments += self.comments
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v.comments += self.comments
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v.save(fname,parallel=False,compress=compress)
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v.save(fname,parallel=False,compress=compress)
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@ -697,14 +702,14 @@ class Grid:
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def show(self,
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def show(self,
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colormap: Colormap = Colormap.from_predefined('cividis')) -> None:
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colormap: Union[Colormap, str] = 'cividis') -> None:
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"""
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"""
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Show on screen.
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Show on screen.
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|
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Parameters
|
Parameters
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----------
|
----------
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colormap : damask.Colormap, optional
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colormap : damask.Colormap or str, optional
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Colors used to map material IDs. Defaults to 'cividis'.
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Colormap for visualization of material IDs. Defaults to 'cividis'.
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|
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"""
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"""
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VTK.from_image_data(self.cells,self.size,self.origin) \
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VTK.from_image_data(self.cells,self.size,self.origin) \
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@ -966,10 +971,10 @@ class Grid:
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extra_keywords = dict(selection=util.tbd(selection),invert=invert_selection)
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extra_keywords = dict(selection=util.tbd(selection),invert=invert_selection)
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material = ndimage.filters.generic_filter(
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material = ndimage.filters.generic_filter(
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self.material,
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self.material,
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mostFrequent,
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mostFrequent,
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size=(stencil if selection is None else stencil//2*2+1,)*3,
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size=(stencil if selection is None else stencil//2*2+1,)*3,
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mode=('wrap' if periodic else 'nearest'),
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mode=('wrap' if periodic else 'nearest'),
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extra_keywords=extra_keywords,
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extra_keywords=extra_keywords,
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).astype(self.material.dtype)
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).astype(self.material.dtype)
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return Grid(material = material,
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return Grid(material = material,
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@ -88,10 +88,10 @@ class VTK:
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@property
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@property
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def comments(self) -> List[str]:
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def comments(self) -> List[str]:
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"""Return the comments."""
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"""Return the comments."""
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fielddata = self.vtk_data.GetFieldData()
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field_data = self.vtk_data.GetFieldData()
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for a in range(fielddata.GetNumberOfArrays()):
|
for a in range(field_data.GetNumberOfArrays()):
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if fielddata.GetArrayName(a) == 'comments':
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if field_data.GetArrayName(a) == 'comments':
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comments = fielddata.GetAbstractArray(a)
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comments = field_data.GetAbstractArray(a)
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return [comments.GetValue(i) for i in range(comments.GetNumberOfValues())]
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return [comments.GetValue(i) for i in range(comments.GetNumberOfValues())]
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return []
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return []
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@ -498,16 +498,26 @@ class VTK:
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# string array
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# string array
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return np.array([vtk_array.GetValue(i) for i in range(vtk_array.GetNumberOfValues())]).astype(str)
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return np.array([vtk_array.GetValue(i) for i in range(vtk_array.GetNumberOfValues())]).astype(str)
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except UnboundLocalError:
|
except UnboundLocalError:
|
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raise ValueError(f'array "{label}" not found')
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raise KeyError(f'array "{label}" not found')
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def show(self,
|
def show(self,
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label: str = None,
|
label: str = None,
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colormap: Colormap = Colormap.from_predefined('cividis')):
|
colormap: Union[Colormap, str] = 'cividis'):
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"""
|
"""
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Render.
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Render.
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||||||
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See http://compilatrix.com/article/vtk-1 for further ideas.
|
Parameters
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||||||
|
----------
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|
label : str, optional
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|
Label of the dataset to show.
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colormap : damask.Colormap or str, optional
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|
Colormap for visualization of dataset. Defaults to 'cividis'.
|
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|
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|
Notes
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|
-----
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||||||
|
See http://compilatrix.com/article/vtk-1 for further ideas.
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||||||
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"""
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"""
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try:
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try:
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import wx
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import wx
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@ -525,8 +535,10 @@ class VTK:
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height = 768
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height = 768
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lut = vtk.vtkLookupTable()
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lut = vtk.vtkLookupTable()
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lut.SetNumberOfTableValues(len(colormap.colors))
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colormap_ = Colormap.from_predefined(colormap) if isinstance(colormap,str) else \
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for i,c in enumerate(colormap.colors):
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colormap
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lut.SetNumberOfTableValues(len(colormap_.colors))
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for i,c in enumerate(colormap_.colors):
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lut.SetTableValue(i,c if len(c)==4 else np.append(c,1.0))
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lut.SetTableValue(i,c if len(c)==4 else np.append(c,1.0))
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lut.Build()
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lut.Build()
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@ -545,11 +557,11 @@ class VTK:
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if label is None:
|
if label is None:
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ren.SetBackground(67/255,128/255,208/255)
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ren.SetBackground(67/255,128/255,208/255)
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else:
|
else:
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colormap = vtk.vtkScalarBarActor()
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colormap_vtk = vtk.vtkScalarBarActor()
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colormap.SetLookupTable(lut)
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colormap_vtk.SetLookupTable(lut)
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colormap.SetTitle(label)
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colormap_vtk.SetTitle(label)
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colormap.SetMaximumWidthInPixels(width//100)
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colormap_vtk.SetMaximumWidthInPixels(width//100)
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ren.AddActor2D(colormap)
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ren.AddActor2D(colormap_vtk)
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ren.SetBackground(0.3,0.3,0.3)
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ren.SetBackground(0.3,0.3,0.3)
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|
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window = vtk.vtkRenderWindow()
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window = vtk.vtkRenderWindow()
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|
|
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||||||
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|
@ -6,6 +6,7 @@ from damask import VTK
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from damask import Grid
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from damask import Grid
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from damask import Table
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from damask import Table
|
||||||
from damask import Rotation
|
from damask import Rotation
|
||||||
|
from damask import Colormap
|
||||||
from damask import util
|
from damask import util
|
||||||
from damask import seeds
|
from damask import seeds
|
||||||
from damask import grid_filters
|
from damask import grid_filters
|
||||||
|
|
@ -50,9 +51,10 @@ class TestGrid:
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||||||
print('patched datetime.datetime.now')
|
print('patched datetime.datetime.now')
|
||||||
|
|
||||||
|
|
||||||
def test_show(sef,default,monkeypatch):
|
@pytest.mark.parametrize('cmap',[Colormap.from_predefined('stress'),'viridis'])
|
||||||
|
def test_show(sef,default,cmap,monkeypatch):
|
||||||
monkeypatch.delenv('DISPLAY',raising=False)
|
monkeypatch.delenv('DISPLAY',raising=False)
|
||||||
default.show()
|
default.show(cmap)
|
||||||
|
|
||||||
def test_equal(self,default):
|
def test_equal(self,default):
|
||||||
assert default == default
|
assert default == default
|
||||||
|
|
@ -69,7 +71,7 @@ class TestGrid:
|
||||||
def test_invalid_no_material(self,tmp_path):
|
def test_invalid_no_material(self,tmp_path):
|
||||||
v = VTK.from_image_data(np.random.randint(5,10,3)*2,np.random.random(3) + 1.0)
|
v = VTK.from_image_data(np.random.randint(5,10,3)*2,np.random.random(3) + 1.0)
|
||||||
v.save(tmp_path/'no_materialpoint.vti',parallel=False)
|
v.save(tmp_path/'no_materialpoint.vti',parallel=False)
|
||||||
with pytest.raises(ValueError):
|
with pytest.raises(KeyError):
|
||||||
Grid.load(tmp_path/'no_materialpoint.vti')
|
Grid.load(tmp_path/'no_materialpoint.vti')
|
||||||
|
|
||||||
def test_invalid_material_type(self):
|
def test_invalid_material_type(self):
|
||||||
|
|
|
||||||
|
|
@ -10,6 +10,7 @@ import vtk
|
||||||
|
|
||||||
from damask import VTK
|
from damask import VTK
|
||||||
from damask import Table
|
from damask import Table
|
||||||
|
from damask import Colormap
|
||||||
|
|
||||||
@pytest.fixture
|
@pytest.fixture
|
||||||
def ref_path(ref_path_base):
|
def ref_path(ref_path_base):
|
||||||
|
|
@ -29,10 +30,10 @@ class TestVTK:
|
||||||
def _patch_execution_stamp(self, patch_execution_stamp):
|
def _patch_execution_stamp(self, patch_execution_stamp):
|
||||||
print('patched damask.util.execution_stamp')
|
print('patched damask.util.execution_stamp')
|
||||||
|
|
||||||
def test_show(sef,default,monkeypatch):
|
@pytest.mark.parametrize('cmap',[Colormap.from_predefined('cividis'),'strain'])
|
||||||
|
def test_show(sef,default,cmap,monkeypatch):
|
||||||
monkeypatch.delenv('DISPLAY',raising=False)
|
monkeypatch.delenv('DISPLAY',raising=False)
|
||||||
default.show()
|
default.show(colormap=cmap)
|
||||||
|
|
||||||
|
|
||||||
def test_imageData(self,tmp_path):
|
def test_imageData(self,tmp_path):
|
||||||
cells = np.random.randint(5,10,3)
|
cells = np.random.randint(5,10,3)
|
||||||
|
|
@ -141,7 +142,7 @@ class TestVTK:
|
||||||
|
|
||||||
|
|
||||||
def test_invalid_get(self,default):
|
def test_invalid_get(self,default):
|
||||||
with pytest.raises(ValueError):
|
with pytest.raises(KeyError):
|
||||||
default.get('does_not_exist')
|
default.get('does_not_exist')
|
||||||
|
|
||||||
def test_invalid_add_shape(self,default):
|
def test_invalid_add_shape(self,default):
|
||||||
|
|
|
||||||
|
|
@ -440,7 +440,7 @@ subroutine IO_error(error_ID,el,ip,g,instance,ext_msg)
|
||||||
case (155)
|
case (155)
|
||||||
msg = 'material index out of bounds'
|
msg = 'material index out of bounds'
|
||||||
case (180)
|
case (180)
|
||||||
msg = 'missing/invalid material definition via State Variable 2'
|
msg = 'missing/invalid material definition'
|
||||||
case (190)
|
case (190)
|
||||||
msg = 'unknown element type:'
|
msg = 'unknown element type:'
|
||||||
case (191)
|
case (191)
|
||||||
|
|
|
||||||
|
|
@ -0,0 +1,446 @@
|
||||||
|
!--------------------------------------------------------------------------------------------------
|
||||||
|
!> @author Martin Diehl, KU Leuven
|
||||||
|
!> @brief Read data from image files of the visualization toolkit.
|
||||||
|
!--------------------------------------------------------------------------------------------------
|
||||||
|
module VTI
|
||||||
|
use prec
|
||||||
|
use zlib
|
||||||
|
use base64
|
||||||
|
use IO
|
||||||
|
|
||||||
|
implicit none
|
||||||
|
private
|
||||||
|
|
||||||
|
public :: &
|
||||||
|
VTI_readDataset_int, &
|
||||||
|
VTI_readDataset_real, &
|
||||||
|
VTI_readCellsSizeOrigin
|
||||||
|
|
||||||
|
contains
|
||||||
|
|
||||||
|
!--------------------------------------------------------------------------------------------------
|
||||||
|
!> @brief Read integer dataset from a VTK image data (*.vti) file.
|
||||||
|
!> @details https://vtk.org/Wiki/VTK_XML_Formats
|
||||||
|
!--------------------------------------------------------------------------------------------------
|
||||||
|
function VTI_readDataset_int(fileContent,label) result(dataset)
|
||||||
|
|
||||||
|
character(len=*), intent(in) :: &
|
||||||
|
label, &
|
||||||
|
fileContent
|
||||||
|
integer, dimension(:), allocatable :: &
|
||||||
|
dataset
|
||||||
|
|
||||||
|
character(len=:), allocatable :: dataType, headerType, base64_str
|
||||||
|
logical :: compressed
|
||||||
|
|
||||||
|
|
||||||
|
call VTI_readDataset_raw(base64_str,dataType,headerType,compressed, &
|
||||||
|
fileContent,label)
|
||||||
|
dataset = as_Int(base64_str,headerType,compressed,dataType)
|
||||||
|
|
||||||
|
if (.not. allocated(dataset)) call IO_error(error_ID = 844, ext_msg='dataset "'//label//'" not found')
|
||||||
|
|
||||||
|
end function VTI_readDataset_int
|
||||||
|
|
||||||
|
|
||||||
|
!--------------------------------------------------------------------------------------------------
|
||||||
|
!> @brief Read real dataset from a VTK image data (*.vti) file.
|
||||||
|
!> @details https://vtk.org/Wiki/VTK_XML_Formats
|
||||||
|
!--------------------------------------------------------------------------------------------------
|
||||||
|
function VTI_readDataset_real(fileContent,label) result(dataset)
|
||||||
|
|
||||||
|
character(len=*), intent(in) :: &
|
||||||
|
label, &
|
||||||
|
fileContent
|
||||||
|
real(pReal), dimension(:), allocatable :: &
|
||||||
|
dataset
|
||||||
|
|
||||||
|
character(len=:), allocatable :: dataType, headerType, base64_str
|
||||||
|
logical :: compressed
|
||||||
|
|
||||||
|
|
||||||
|
call VTI_readDataset_raw(base64_str,dataType,headerType,compressed, &
|
||||||
|
fileContent,label)
|
||||||
|
dataset = as_real(base64_str,headerType,compressed,dataType)
|
||||||
|
|
||||||
|
if (.not. allocated(dataset)) call IO_error(error_ID = 844, ext_msg='dataset "'//label//'" not found')
|
||||||
|
|
||||||
|
end function VTI_readDataset_real
|
||||||
|
|
||||||
|
|
||||||
|
!--------------------------------------------------------------------------------------------------
|
||||||
|
!> @brief Read dataset as raw data (base64 string) from a VTK image data (*.vti) file.
|
||||||
|
!> @details https://vtk.org/Wiki/VTK_XML_Formats
|
||||||
|
!--------------------------------------------------------------------------------------------------
|
||||||
|
subroutine VTI_readDataset_raw(base64_str,dataType,headerType,compressed, &
|
||||||
|
fileContent,label)
|
||||||
|
|
||||||
|
character(len=*), intent(in) :: &
|
||||||
|
label, &
|
||||||
|
fileContent
|
||||||
|
character(len=:), allocatable, intent(out) :: dataType, headerType, base64_str
|
||||||
|
logical, intent(out) :: compressed
|
||||||
|
|
||||||
|
logical :: inFile,inImage,gotCellData
|
||||||
|
integer(pI64) :: &
|
||||||
|
startPos, endPos, &
|
||||||
|
s
|
||||||
|
|
||||||
|
|
||||||
|
inFile = .false.
|
||||||
|
inImage = .false.
|
||||||
|
startPos = 1_pI64
|
||||||
|
outer: do while (startPos < len(fileContent,kind=pI64))
|
||||||
|
endPos = startPos + index(fileContent(startPos:),IO_EOL,kind=pI64) - 2_pI64
|
||||||
|
if (endPos < startPos) endPos = len(fileContent,kind=pI64) ! end of file without new line
|
||||||
|
|
||||||
|
if (.not. inFile) then
|
||||||
|
if (index(fileContent(startPos:endPos),'<VTKFile',kind=pI64) /= 0_pI64) then
|
||||||
|
inFile = .true.
|
||||||
|
if (.not. fileFormatOk(fileContent(startPos:endPos))) call IO_error(error_ID = 844, ext_msg='file format')
|
||||||
|
headerType = merge('UInt64','UInt32',getXMLValue(fileContent(startPos:endPos),'header_type')=='UInt64')
|
||||||
|
compressed = getXMLValue(fileContent(startPos:endPos),'compressor') == 'vtkZLibDataCompressor'
|
||||||
|
end if
|
||||||
|
else
|
||||||
|
if (.not. inImage) then
|
||||||
|
if (index(fileContent(startPos:endPos),'<ImageData',kind=pI64) /= 0_pI64) then
|
||||||
|
inImage = .true.
|
||||||
|
end if
|
||||||
|
else
|
||||||
|
if (index(fileContent(startPos:endPos),'<CellData',kind=pI64) /= 0_pI64) then
|
||||||
|
do while (index(fileContent(startPos:endPos),'</CellData>',kind=pI64) == 0_pI64)
|
||||||
|
if (index(fileContent(startPos:endPos),'<DataArray',kind=pI64) /= 0_pI64 .and. &
|
||||||
|
getXMLValue(fileContent(startPos:endPos),'Name') == label ) then
|
||||||
|
|
||||||
|
if (getXMLValue(fileContent(startPos:endPos),'format') /= 'binary') &
|
||||||
|
call IO_error(error_ID = 844, ext_msg='format ('//label//')')
|
||||||
|
dataType = getXMLValue(fileContent(startPos:endPos),'type')
|
||||||
|
|
||||||
|
startPos = endPos + 2_pI64
|
||||||
|
endPos = startPos + index(fileContent(startPos:),IO_EOL,kind=pI64) - 2_pI64
|
||||||
|
s = startPos + verify(fileContent(startPos:endPos),IO_WHITESPACE,kind=pI64) -1_pI64 ! start (no leading whitespace)
|
||||||
|
base64_str = fileContent(s:endPos)
|
||||||
|
exit outer
|
||||||
|
end if
|
||||||
|
startPos = endPos + 2_pI64
|
||||||
|
endPos = startPos + index(fileContent(startPos:),IO_EOL,kind=pI64) - 2_pI64
|
||||||
|
end do
|
||||||
|
end if
|
||||||
|
end if
|
||||||
|
end if
|
||||||
|
|
||||||
|
startPos = endPos + 2_pI64
|
||||||
|
|
||||||
|
end do outer
|
||||||
|
|
||||||
|
end subroutine VTI_readDataset_raw
|
||||||
|
|
||||||
|
|
||||||
|
!--------------------------------------------------------------------------------------------------
|
||||||
|
!> @brief Read cells, size, and origin of an VTK image data (*.vti) file.
|
||||||
|
!> @details https://vtk.org/Wiki/VTK_XML_Formats
|
||||||
|
!--------------------------------------------------------------------------------------------------
|
||||||
|
subroutine VTI_readCellsSizeOrigin(cells,geomSize,origin, &
|
||||||
|
fileContent)
|
||||||
|
|
||||||
|
integer, dimension(3), intent(out) :: &
|
||||||
|
cells ! # of cells (across all processes!)
|
||||||
|
real(pReal), dimension(3), intent(out) :: &
|
||||||
|
geomSize, & ! size (across all processes!)
|
||||||
|
origin ! origin (across all processes!)
|
||||||
|
character(len=*), intent(in) :: &
|
||||||
|
fileContent
|
||||||
|
|
||||||
|
character(len=:), allocatable :: dataType, headerType
|
||||||
|
logical :: inFile,inImage,gotCellData,compressed
|
||||||
|
integer(pI64) :: &
|
||||||
|
startPos, endPos, &
|
||||||
|
s
|
||||||
|
|
||||||
|
|
||||||
|
cells = -1
|
||||||
|
geomSize = -1.0_pReal
|
||||||
|
|
||||||
|
inFile = .false.
|
||||||
|
inImage = .false.
|
||||||
|
startPos = 1_pI64
|
||||||
|
outer: do while (startPos < len(fileContent,kind=pI64))
|
||||||
|
endPos = startPos + index(fileContent(startPos:),IO_EOL,kind=pI64) - 2_pI64
|
||||||
|
if (endPos < startPos) endPos = len(fileContent,kind=pI64) ! end of file without new line
|
||||||
|
|
||||||
|
if (.not. inFile) then
|
||||||
|
if (index(fileContent(startPos:endPos),'<VTKFile',kind=pI64) /= 0_pI64) then
|
||||||
|
inFile = .true.
|
||||||
|
if (.not. fileFormatOk(fileContent(startPos:endPos))) call IO_error(error_ID = 844, ext_msg='file format')
|
||||||
|
headerType = merge('UInt64','UInt32',getXMLValue(fileContent(startPos:endPos),'header_type')=='UInt64')
|
||||||
|
compressed = getXMLValue(fileContent(startPos:endPos),'compressor') == 'vtkZLibDataCompressor'
|
||||||
|
end if
|
||||||
|
else
|
||||||
|
if (.not. inImage) then
|
||||||
|
if (index(fileContent(startPos:endPos),'<ImageData',kind=pI64) /= 0_pI64) then
|
||||||
|
inImage = .true.
|
||||||
|
call cellsSizeOrigin(cells,geomSize,origin,fileContent(startPos:endPos))
|
||||||
|
exit outer
|
||||||
|
end if
|
||||||
|
end if
|
||||||
|
end if
|
||||||
|
|
||||||
|
startPos = endPos + 2_pI64
|
||||||
|
|
||||||
|
end do outer
|
||||||
|
|
||||||
|
if (any(geomSize<=0)) call IO_error(error_ID = 844, ext_msg='size')
|
||||||
|
if (any(cells<1)) call IO_error(error_ID = 844, ext_msg='cells')
|
||||||
|
|
||||||
|
end subroutine VTI_readCellsSizeOrigin
|
||||||
|
|
||||||
|
|
||||||
|
!--------------------------------------------------------------------------------------------------
|
||||||
|
!> @brief Determine size and origin from coordinates.
|
||||||
|
!--------------------------------------------------------------------------------------------------
|
||||||
|
subroutine cellsSizeOrigin(c,s,o,header)
|
||||||
|
|
||||||
|
integer, dimension(3), intent(out) :: c
|
||||||
|
real(pReal), dimension(3), intent(out) :: s,o
|
||||||
|
character(len=*), intent(in) :: header
|
||||||
|
|
||||||
|
character(len=:), allocatable :: temp
|
||||||
|
real(pReal), dimension(3) :: delta
|
||||||
|
integer :: i
|
||||||
|
|
||||||
|
|
||||||
|
temp = getXMLValue(header,'Direction')
|
||||||
|
if (temp /= '1 0 0 0 1 0 0 0 1' .and. temp /= '') & ! https://discourse.vtk.org/t/vti-specification/6526
|
||||||
|
call IO_error(error_ID = 844, ext_msg = 'coordinate order')
|
||||||
|
|
||||||
|
temp = getXMLValue(header,'WholeExtent')
|
||||||
|
if (any([(IO_intValue(temp,IO_stringPos(temp),i),i=1,5,2)] /= 0)) &
|
||||||
|
call IO_error(error_ID = 844, ext_msg = 'coordinate start')
|
||||||
|
c = [(IO_intValue(temp,IO_stringPos(temp),i),i=2,6,2)]
|
||||||
|
|
||||||
|
temp = getXMLValue(header,'Spacing')
|
||||||
|
delta = [(IO_floatValue(temp,IO_stringPos(temp),i),i=1,3)]
|
||||||
|
s = delta * real(c,pReal)
|
||||||
|
|
||||||
|
temp = getXMLValue(header,'Origin')
|
||||||
|
o = [(IO_floatValue(temp,IO_stringPos(temp),i),i=1,3)]
|
||||||
|
|
||||||
|
end subroutine
|
||||||
|
|
||||||
|
|
||||||
|
!--------------------------------------------------------------------------------------------------
|
||||||
|
!> @brief Interpret Base64 string in vtk XML file as integer of default kind.
|
||||||
|
!--------------------------------------------------------------------------------------------------
|
||||||
|
function as_Int(base64_str,headerType,compressed,dataType)
|
||||||
|
|
||||||
|
character(len=*), intent(in) :: base64_str, & ! base64 encoded string
|
||||||
|
headerType, & ! header type (UInt32 or Uint64)
|
||||||
|
dataType ! data type (Int32, Int64, Float32, Float64)
|
||||||
|
logical, intent(in) :: compressed ! indicate whether data is zlib compressed
|
||||||
|
|
||||||
|
integer, dimension(:), allocatable :: as_Int
|
||||||
|
|
||||||
|
|
||||||
|
select case(dataType)
|
||||||
|
case('Int32')
|
||||||
|
as_Int = int(prec_bytesToC_INT32_T(asBytes(base64_str,headerType,compressed)))
|
||||||
|
case('Int64')
|
||||||
|
as_Int = int(prec_bytesToC_INT64_T(asBytes(base64_str,headerType,compressed)))
|
||||||
|
case('Float32')
|
||||||
|
as_Int = int(prec_bytesToC_FLOAT (asBytes(base64_str,headerType,compressed)))
|
||||||
|
case('Float64')
|
||||||
|
as_Int = int(prec_bytesToC_DOUBLE (asBytes(base64_str,headerType,compressed)))
|
||||||
|
case default
|
||||||
|
call IO_error(844,ext_msg='unknown data type: '//trim(dataType))
|
||||||
|
end select
|
||||||
|
|
||||||
|
end function as_Int
|
||||||
|
|
||||||
|
|
||||||
|
!--------------------------------------------------------------------------------------------------
|
||||||
|
!> @brief Interpret Base64 string in vtk XML file as real of kind pReal.
|
||||||
|
!--------------------------------------------------------------------------------------------------
|
||||||
|
function as_real(base64_str,headerType,compressed,dataType)
|
||||||
|
|
||||||
|
character(len=*), intent(in) :: base64_str, & ! base64 encoded string
|
||||||
|
headerType, & ! header type (UInt32 or Uint64)
|
||||||
|
dataType ! data type (Int32, Int64, Float32, Float64)
|
||||||
|
logical, intent(in) :: compressed ! indicate whether data is zlib compressed
|
||||||
|
|
||||||
|
real(pReal), dimension(:), allocatable :: as_real
|
||||||
|
|
||||||
|
|
||||||
|
select case(dataType)
|
||||||
|
case('Int32')
|
||||||
|
as_real = real(prec_bytesToC_INT32_T(asBytes(base64_str,headerType,compressed)),pReal)
|
||||||
|
case('Int64')
|
||||||
|
as_real = real(prec_bytesToC_INT64_T(asBytes(base64_str,headerType,compressed)),pReal)
|
||||||
|
case('Float32')
|
||||||
|
as_real = real(prec_bytesToC_FLOAT (asBytes(base64_str,headerType,compressed)),pReal)
|
||||||
|
case('Float64')
|
||||||
|
as_real = real(prec_bytesToC_DOUBLE (asBytes(base64_str,headerType,compressed)),pReal)
|
||||||
|
case default
|
||||||
|
call IO_error(844,ext_msg='unknown data type: '//trim(dataType))
|
||||||
|
end select
|
||||||
|
|
||||||
|
end function as_real
|
||||||
|
|
||||||
|
|
||||||
|
!--------------------------------------------------------------------------------------------------
|
||||||
|
!> @brief Interpret Base64 string in vtk XML file as bytes.
|
||||||
|
!--------------------------------------------------------------------------------------------------
|
||||||
|
function asBytes(base64_str,headerType,compressed) result(bytes)
|
||||||
|
|
||||||
|
character(len=*), intent(in) :: base64_str, & ! base64 encoded string
|
||||||
|
headerType ! header type (UInt32 or Uint64)
|
||||||
|
logical, intent(in) :: compressed ! indicate whether data is zlib compressed
|
||||||
|
|
||||||
|
integer(C_SIGNED_CHAR), dimension(:), allocatable :: bytes
|
||||||
|
|
||||||
|
|
||||||
|
if (compressed) then
|
||||||
|
bytes = asBytes_compressed(base64_str,headerType)
|
||||||
|
else
|
||||||
|
bytes = asBytes_uncompressed(base64_str,headerType)
|
||||||
|
end if
|
||||||
|
|
||||||
|
end function asBytes
|
||||||
|
|
||||||
|
|
||||||
|
!--------------------------------------------------------------------------------------------------
|
||||||
|
!> @brief Interpret compressed Base64 string in vtk XML file as bytes.
|
||||||
|
!> @details A compressed Base64 string consists of a header block and a data block
|
||||||
|
! [#blocks/#u-size/#p-size/#c-size-1/#c-size-2/.../#c-size-#blocks][DATA-1/DATA-2...]
|
||||||
|
! #blocks = Number of blocks
|
||||||
|
! #u-size = Block size before compression
|
||||||
|
! #p-size = Size of last partial block (zero if it not needed)
|
||||||
|
! #c-size-i = Size in bytes of block i after compression
|
||||||
|
!--------------------------------------------------------------------------------------------------
|
||||||
|
function asBytes_compressed(base64_str,headerType) result(bytes)
|
||||||
|
|
||||||
|
character(len=*), intent(in) :: base64_str, & ! base64 encoded string
|
||||||
|
headerType ! header type (UInt32 or Uint64)
|
||||||
|
integer(C_SIGNED_CHAR), dimension(:), allocatable :: bytes
|
||||||
|
|
||||||
|
integer(C_SIGNED_CHAR), dimension(:), allocatable :: bytes_inflated
|
||||||
|
integer(pI64), dimension(:), allocatable :: temp, size_inflated, size_deflated
|
||||||
|
integer(pI64) :: headerLen, nBlock, b,s,e
|
||||||
|
|
||||||
|
|
||||||
|
if (headerType == 'UInt32') then
|
||||||
|
temp = int(prec_bytesToC_INT32_T(base64_to_bytes(base64_str(:base64_nChar(4_pI64)))),pI64)
|
||||||
|
nBlock = int(temp(1),pI64)
|
||||||
|
headerLen = 4_pI64 * (3_pI64 + nBlock)
|
||||||
|
temp = int(prec_bytesToC_INT32_T(base64_to_bytes(base64_str(:base64_nChar(headerLen)))),pI64)
|
||||||
|
else if (headerType == 'UInt64') then
|
||||||
|
temp = int(prec_bytesToC_INT64_T(base64_to_bytes(base64_str(:base64_nChar(8_pI64)))),pI64)
|
||||||
|
nBlock = int(temp(1),pI64)
|
||||||
|
headerLen = 8_pI64 * (3_pI64 + nBlock)
|
||||||
|
temp = int(prec_bytesToC_INT64_T(base64_to_bytes(base64_str(:base64_nChar(headerLen)))),pI64)
|
||||||
|
end if
|
||||||
|
|
||||||
|
allocate(size_inflated(nBlock),source=temp(2))
|
||||||
|
size_inflated(nBlock) = merge(temp(3),temp(2),temp(3)/=0_pI64)
|
||||||
|
size_deflated = temp(4:)
|
||||||
|
bytes_inflated = base64_to_bytes(base64_str(base64_nChar(headerLen)+1_pI64:))
|
||||||
|
|
||||||
|
allocate(bytes(sum(size_inflated)))
|
||||||
|
e = 0_pI64
|
||||||
|
do b = 1, nBlock
|
||||||
|
s = e + 1_pI64
|
||||||
|
e = s + size_deflated(b) - 1_pI64
|
||||||
|
bytes(sum(size_inflated(:b-1))+1_pI64:sum(size_inflated(:b))) = zlib_inflate(bytes_inflated(s:e),size_inflated(b))
|
||||||
|
end do
|
||||||
|
|
||||||
|
end function asBytes_compressed
|
||||||
|
|
||||||
|
|
||||||
|
!--------------------------------------------------------------------------------------------------
|
||||||
|
!> @brief Interprete uncompressed Base64 string in vtk XML file as bytes.
|
||||||
|
!> @details An uncompressed Base64 string consists of N headers blocks and a N data blocks
|
||||||
|
![#bytes-1/DATA-1][#bytes-2/DATA-2]...
|
||||||
|
!--------------------------------------------------------------------------------------------------
|
||||||
|
function asBytes_uncompressed(base64_str,headerType) result(bytes)
|
||||||
|
|
||||||
|
character(len=*), intent(in) :: base64_str, & ! base64 encoded string
|
||||||
|
headerType ! header type (UInt32 or Uint64)
|
||||||
|
integer(C_SIGNED_CHAR), dimension(:), allocatable :: bytes
|
||||||
|
|
||||||
|
integer(pI64) :: s
|
||||||
|
integer(pI64), dimension(1) :: nByte
|
||||||
|
|
||||||
|
|
||||||
|
allocate(bytes(0))
|
||||||
|
|
||||||
|
s=0_pI64
|
||||||
|
if (headerType == 'UInt32') then
|
||||||
|
do while(s+base64_nChar(4_pI64)<(len(base64_str,pI64)))
|
||||||
|
nByte = int(prec_bytesToC_INT32_T(base64_to_bytes(base64_str(s+1_pI64:s+base64_nChar(4_pI64)))),pI64)
|
||||||
|
bytes = [bytes,base64_to_bytes(base64_str(s+1_pI64:s+base64_nChar(4_pI64+nByte(1))),5_pI64)]
|
||||||
|
s = s + base64_nChar(4_pI64+nByte(1))
|
||||||
|
end do
|
||||||
|
else if (headerType == 'UInt64') then
|
||||||
|
do while(s+base64_nChar(8_pI64)<(len(base64_str,pI64)))
|
||||||
|
nByte = int(prec_bytesToC_INT64_T(base64_to_bytes(base64_str(s+1_pI64:s+base64_nChar(8_pI64)))),pI64)
|
||||||
|
bytes = [bytes,base64_to_bytes(base64_str(s+1_pI64:s+base64_nChar(8_pI64+nByte(1))),9_pI64)]
|
||||||
|
s = s + base64_nChar(8_pI64+nByte(1))
|
||||||
|
end do
|
||||||
|
end if
|
||||||
|
|
||||||
|
end function asBytes_uncompressed
|
||||||
|
|
||||||
|
|
||||||
|
!--------------------------------------------------------------------------------------------------
|
||||||
|
!> @brief Get XML string value for given key.
|
||||||
|
!--------------------------------------------------------------------------------------------------
|
||||||
|
pure function getXMLValue(line,key)
|
||||||
|
|
||||||
|
character(len=*), intent(in) :: line, key
|
||||||
|
character(len=:), allocatable :: getXMLValue
|
||||||
|
|
||||||
|
integer :: s,e
|
||||||
|
#ifdef __INTEL_COMPILER
|
||||||
|
character :: q
|
||||||
|
#endif
|
||||||
|
|
||||||
|
|
||||||
|
s = index(line," "//key,back=.true.)
|
||||||
|
if (s==0) then
|
||||||
|
getXMLValue = ''
|
||||||
|
else
|
||||||
|
e = s + 1 + scan(line(s+1:),"'"//'"')
|
||||||
|
if (scan(line(s:e-2),'=') == 0) then
|
||||||
|
getXMLValue = ''
|
||||||
|
else
|
||||||
|
s = e
|
||||||
|
!https://community.intel.com/t5/Intel-Fortran-Compiler/ICE-for-merge-with-strings/m-p/1207204#M151657
|
||||||
|
#ifdef __INTEL_COMPILER
|
||||||
|
q = line(s-1:s-1)
|
||||||
|
e = s + index(line(s:),q) - 1
|
||||||
|
#else
|
||||||
|
e = s + index(line(s:),merge("'",'"',line(s-1:s-1)=="'")) - 1
|
||||||
|
#endif
|
||||||
|
getXMLValue = line(s:e-1)
|
||||||
|
end if
|
||||||
|
end if
|
||||||
|
|
||||||
|
end function
|
||||||
|
|
||||||
|
|
||||||
|
!--------------------------------------------------------------------------------------------------
|
||||||
|
!> @brief Check for supported file format variants.
|
||||||
|
!--------------------------------------------------------------------------------------------------
|
||||||
|
pure function fileFormatOk(line)
|
||||||
|
|
||||||
|
character(len=*),intent(in) :: line
|
||||||
|
logical :: fileFormatOk
|
||||||
|
|
||||||
|
|
||||||
|
fileFormatOk = getXMLValue(line,'type') == 'ImageData' .and. &
|
||||||
|
getXMLValue(line,'byte_order') == 'LittleEndian' .and. &
|
||||||
|
getXMLValue(line,'compressor') /= 'vtkLZ4DataCompressor' .and. &
|
||||||
|
getXMLValue(line,'compressor') /= 'vtkLZMADataCompressor'
|
||||||
|
|
||||||
|
end function fileFormatOk
|
||||||
|
|
||||||
|
end module VTI
|
||||||
|
|
@ -14,8 +14,7 @@ module discretization_grid
|
||||||
use prec
|
use prec
|
||||||
use parallelization
|
use parallelization
|
||||||
use system_routines
|
use system_routines
|
||||||
use base64
|
use VTI
|
||||||
use zlib
|
|
||||||
use DAMASK_interface
|
use DAMASK_interface
|
||||||
use IO
|
use IO
|
||||||
use config
|
use config
|
||||||
|
|
@ -77,7 +76,12 @@ subroutine discretization_grid_init(restart)
|
||||||
|
|
||||||
if (worldrank == 0) then
|
if (worldrank == 0) then
|
||||||
fileContent = IO_read(interface_geomFile)
|
fileContent = IO_read(interface_geomFile)
|
||||||
call readVTI(cells,geomSize,origin,materialAt_global,fileContent)
|
call VTI_readCellsSizeOrigin(cells,geomSize,origin,fileContent)
|
||||||
|
materialAt_global = VTI_readDataset_int(fileContent,'material') + 1
|
||||||
|
if (any(materialAt_global < 1)) &
|
||||||
|
call IO_error(180,ext_msg='material ID < 1')
|
||||||
|
if (size(materialAt_global) /= product(cells)) &
|
||||||
|
call IO_error(180,ext_msg='mismatch in # of material IDs and cells')
|
||||||
fname = interface_geomFile
|
fname = interface_geomFile
|
||||||
if (scan(fname,'/') /= 0) fname = fname(scan(fname,'/',.true.)+1:)
|
if (scan(fname,'/') /= 0) fname = fname(scan(fname,'/',.true.)+1:)
|
||||||
call results_openJobFile(parallel=.false.)
|
call results_openJobFile(parallel=.false.)
|
||||||
|
|
@ -166,339 +170,6 @@ subroutine discretization_grid_init(restart)
|
||||||
end subroutine discretization_grid_init
|
end subroutine discretization_grid_init
|
||||||
|
|
||||||
|
|
||||||
!--------------------------------------------------------------------------------------------------
|
|
||||||
!> @brief Parse vtk image data (.vti)
|
|
||||||
!> @details https://vtk.org/Wiki/VTK_XML_Formats
|
|
||||||
!--------------------------------------------------------------------------------------------------
|
|
||||||
subroutine readVTI(cells,geomSize,origin,material, &
|
|
||||||
fileContent)
|
|
||||||
|
|
||||||
integer, dimension(3), intent(out) :: &
|
|
||||||
cells ! cells (across all processes!)
|
|
||||||
real(pReal), dimension(3), intent(out) :: &
|
|
||||||
geomSize, & ! size (across all processes!)
|
|
||||||
origin ! origin (across all processes!)
|
|
||||||
integer, dimension(:), intent(out), allocatable :: &
|
|
||||||
material
|
|
||||||
character(len=*), intent(in) :: &
|
|
||||||
fileContent
|
|
||||||
|
|
||||||
character(len=:), allocatable :: dataType, headerType
|
|
||||||
logical :: inFile,inImage,gotCellData,compressed
|
|
||||||
integer(pI64) :: &
|
|
||||||
startPos, endPos, &
|
|
||||||
s
|
|
||||||
|
|
||||||
|
|
||||||
cells = -1
|
|
||||||
geomSize = -1.0_pReal
|
|
||||||
|
|
||||||
inFile = .false.
|
|
||||||
inImage = .false.
|
|
||||||
gotCelldata = .false.
|
|
||||||
|
|
||||||
!--------------------------------------------------------------------------------------------------
|
|
||||||
! parse XML file
|
|
||||||
startPos = 1_pI64
|
|
||||||
do while (startPos < len(fileContent,kind=pI64))
|
|
||||||
endPos = startPos + index(fileContent(startPos:),IO_EOL,kind=pI64) - 2_pI64
|
|
||||||
if (endPos < startPos) endPos = len(fileContent,kind=pI64) ! end of file without new line
|
|
||||||
|
|
||||||
if (.not. inFile) then
|
|
||||||
if (index(fileContent(startPos:endPos),'<VTKFile',kind=pI64) /= 0_pI64) then
|
|
||||||
inFile = .true.
|
|
||||||
if (.not. fileFormatOk(fileContent(startPos:endPos))) call IO_error(error_ID = 844, ext_msg='file format')
|
|
||||||
headerType = merge('UInt64','UInt32',getXMLValue(fileContent(startPos:endPos),'header_type')=='UInt64')
|
|
||||||
compressed = getXMLValue(fileContent(startPos:endPos),'compressor') == 'vtkZLibDataCompressor'
|
|
||||||
end if
|
|
||||||
else
|
|
||||||
if (.not. inImage) then
|
|
||||||
if (index(fileContent(startPos:endPos),'<ImageData',kind=pI64) /= 0_pI64) then
|
|
||||||
inImage = .true.
|
|
||||||
call cellsSizeOrigin(cells,geomSize,origin,fileContent(startPos:endPos))
|
|
||||||
end if
|
|
||||||
else
|
|
||||||
if (index(fileContent(startPos:endPos),'<CellData',kind=pI64) /= 0_pI64) then
|
|
||||||
gotCellData = .true.
|
|
||||||
do while (index(fileContent(startPos:endPos),'</CellData>',kind=pI64) == 0_pI64)
|
|
||||||
if (index(fileContent(startPos:endPos),'<DataArray',kind=pI64) /= 0_pI64 .and. &
|
|
||||||
getXMLValue(fileContent(startPos:endPos),'Name') == 'material' ) then
|
|
||||||
|
|
||||||
if (getXMLValue(fileContent(startPos:endPos),'format') /= 'binary') &
|
|
||||||
call IO_error(error_ID = 844, ext_msg='format (material)')
|
|
||||||
dataType = getXMLValue(fileContent(startPos:endPos),'type')
|
|
||||||
|
|
||||||
startPos = endPos + 2_pI64
|
|
||||||
endPos = startPos + index(fileContent(startPos:),IO_EOL,kind=pI64) - 2_pI64
|
|
||||||
s = startPos + verify(fileContent(startPos:endPos),IO_WHITESPACE,kind=pI64) -1_pI64 ! start (no leading whitespace)
|
|
||||||
material = as_Int(fileContent(s:endPos),headerType,compressed,dataType)
|
|
||||||
exit
|
|
||||||
end if
|
|
||||||
startPos = endPos + 2_pI64
|
|
||||||
endPos = startPos + index(fileContent(startPos:),IO_EOL,kind=pI64) - 2_pI64
|
|
||||||
end do
|
|
||||||
end if
|
|
||||||
end if
|
|
||||||
end if
|
|
||||||
|
|
||||||
if (gotCellData) exit
|
|
||||||
startPos = endPos + 2_pI64
|
|
||||||
|
|
||||||
end do
|
|
||||||
|
|
||||||
if (.not. allocated(material)) call IO_error(error_ID = 844, ext_msg='material data not found')
|
|
||||||
if (size(material) /= product(cells)) call IO_error(error_ID = 844, ext_msg='size(material)')
|
|
||||||
if (any(geomSize<=0)) call IO_error(error_ID = 844, ext_msg='size')
|
|
||||||
if (any(cells<1)) call IO_error(error_ID = 844, ext_msg='cells')
|
|
||||||
material = material + 1
|
|
||||||
if (any(material<1)) call IO_error(error_ID = 844, ext_msg='material ID < 0')
|
|
||||||
|
|
||||||
contains
|
|
||||||
|
|
||||||
!------------------------------------------------------------------------------------------------
|
|
||||||
!> @brief determine size and origin from coordinates
|
|
||||||
!------------------------------------------------------------------------------------------------
|
|
||||||
subroutine cellsSizeOrigin(c,s,o,header)
|
|
||||||
|
|
||||||
integer, dimension(3), intent(out) :: c
|
|
||||||
real(pReal), dimension(3), intent(out) :: s,o
|
|
||||||
character(len=*), intent(in) :: header
|
|
||||||
|
|
||||||
character(len=:), allocatable :: temp
|
|
||||||
real(pReal), dimension(:), allocatable :: delta
|
|
||||||
integer :: i
|
|
||||||
|
|
||||||
|
|
||||||
temp = getXMLValue(header,'Direction')
|
|
||||||
if (temp /= '1 0 0 0 1 0 0 0 1' .and. temp /= '') & ! https://discourse.vtk.org/t/vti-specification/6526
|
|
||||||
call IO_error(error_ID = 844, ext_msg = 'coordinate order')
|
|
||||||
|
|
||||||
temp = getXMLValue(header,'WholeExtent')
|
|
||||||
if (any([(IO_intValue(temp,IO_stringPos(temp),i),i=1,5,2)] /= 0)) &
|
|
||||||
call IO_error(error_ID = 844, ext_msg = 'coordinate start')
|
|
||||||
c = [(IO_intValue(temp,IO_stringPos(temp),i),i=2,6,2)]
|
|
||||||
|
|
||||||
temp = getXMLValue(header,'Spacing')
|
|
||||||
delta = [(IO_floatValue(temp,IO_stringPos(temp),i),i=1,3)]
|
|
||||||
s = delta * real(c,pReal)
|
|
||||||
|
|
||||||
temp = getXMLValue(header,'Origin')
|
|
||||||
o = [(IO_floatValue(temp,IO_stringPos(temp),i),i=1,3)]
|
|
||||||
|
|
||||||
end subroutine
|
|
||||||
|
|
||||||
|
|
||||||
!------------------------------------------------------------------------------------------------
|
|
||||||
!> @brief Interpret Base64 string in vtk XML file as integer of default kind
|
|
||||||
!------------------------------------------------------------------------------------------------
|
|
||||||
function as_Int(base64_str,headerType,compressed,dataType)
|
|
||||||
|
|
||||||
character(len=*), intent(in) :: base64_str, & ! base64 encoded string
|
|
||||||
headerType, & ! header type (UInt32 or Uint64)
|
|
||||||
dataType ! data type (Int32, Int64, Float32, Float64)
|
|
||||||
logical, intent(in) :: compressed ! indicate whether data is zlib compressed
|
|
||||||
|
|
||||||
integer, dimension(:), allocatable :: as_Int
|
|
||||||
|
|
||||||
select case(dataType)
|
|
||||||
case('Int32')
|
|
||||||
as_Int = int(prec_bytesToC_INT32_T(asBytes(base64_str,headerType,compressed)))
|
|
||||||
case('Int64')
|
|
||||||
as_Int = int(prec_bytesToC_INT64_T(asBytes(base64_str,headerType,compressed)))
|
|
||||||
case('Float32')
|
|
||||||
as_Int = int(prec_bytesToC_FLOAT (asBytes(base64_str,headerType,compressed)))
|
|
||||||
case('Float64')
|
|
||||||
as_Int = int(prec_bytesToC_DOUBLE (asBytes(base64_str,headerType,compressed)))
|
|
||||||
case default
|
|
||||||
call IO_error(844,ext_msg='unknown data type: '//trim(dataType))
|
|
||||||
end select
|
|
||||||
|
|
||||||
end function as_Int
|
|
||||||
|
|
||||||
|
|
||||||
!------------------------------------------------------------------------------------------------
|
|
||||||
!> @brief Interpret Base64 string in vtk XML file as integer of pReal kind
|
|
||||||
!------------------------------------------------------------------------------------------------
|
|
||||||
function as_pReal(base64_str,headerType,compressed,dataType)
|
|
||||||
|
|
||||||
character(len=*), intent(in) :: base64_str, & ! base64 encoded string
|
|
||||||
headerType, & ! header type (UInt32 or Uint64)
|
|
||||||
dataType ! data type (Int32, Int64, Float32, Float64)
|
|
||||||
logical, intent(in) :: compressed ! indicate whether data is zlib compressed
|
|
||||||
|
|
||||||
real(pReal), dimension(:), allocatable :: as_pReal
|
|
||||||
|
|
||||||
select case(dataType)
|
|
||||||
case('Int32')
|
|
||||||
as_pReal = real(prec_bytesToC_INT32_T(asBytes(base64_str,headerType,compressed)),pReal)
|
|
||||||
case('Int64')
|
|
||||||
as_pReal = real(prec_bytesToC_INT64_T(asBytes(base64_str,headerType,compressed)),pReal)
|
|
||||||
case('Float32')
|
|
||||||
as_pReal = real(prec_bytesToC_FLOAT (asBytes(base64_str,headerType,compressed)),pReal)
|
|
||||||
case('Float64')
|
|
||||||
as_pReal = real(prec_bytesToC_DOUBLE (asBytes(base64_str,headerType,compressed)),pReal)
|
|
||||||
case default
|
|
||||||
call IO_error(844,ext_msg='unknown data type: '//trim(dataType))
|
|
||||||
end select
|
|
||||||
|
|
||||||
end function as_pReal
|
|
||||||
|
|
||||||
|
|
||||||
!------------------------------------------------------------------------------------------------
|
|
||||||
!> @brief Interpret Base64 string in vtk XML file as bytes
|
|
||||||
!------------------------------------------------------------------------------------------------
|
|
||||||
function asBytes(base64_str,headerType,compressed) result(bytes)
|
|
||||||
|
|
||||||
character(len=*), intent(in) :: base64_str, & ! base64 encoded string
|
|
||||||
headerType ! header type (UInt32 or Uint64)
|
|
||||||
logical, intent(in) :: compressed ! indicate whether data is zlib compressed
|
|
||||||
|
|
||||||
integer(C_SIGNED_CHAR), dimension(:), allocatable :: bytes
|
|
||||||
|
|
||||||
if (compressed) then
|
|
||||||
bytes = asBytes_compressed(base64_str,headerType)
|
|
||||||
else
|
|
||||||
bytes = asBytes_uncompressed(base64_str,headerType)
|
|
||||||
end if
|
|
||||||
|
|
||||||
end function asBytes
|
|
||||||
|
|
||||||
!------------------------------------------------------------------------------------------------
|
|
||||||
!> @brief Interpret compressed Base64 string in vtk XML file as bytes
|
|
||||||
!> @details A compressed Base64 string consists of a header block and a data block
|
|
||||||
! [#blocks/#u-size/#p-size/#c-size-1/#c-size-2/.../#c-size-#blocks][DATA-1/DATA-2...]
|
|
||||||
! #blocks = Number of blocks
|
|
||||||
! #u-size = Block size before compression
|
|
||||||
! #p-size = Size of last partial block (zero if it not needed)
|
|
||||||
! #c-size-i = Size in bytes of block i after compression
|
|
||||||
!------------------------------------------------------------------------------------------------
|
|
||||||
function asBytes_compressed(base64_str,headerType) result(bytes)
|
|
||||||
|
|
||||||
character(len=*), intent(in) :: base64_str, & ! base64 encoded string
|
|
||||||
headerType ! header type (UInt32 or Uint64)
|
|
||||||
|
|
||||||
integer(C_SIGNED_CHAR), dimension(:), allocatable :: bytes, bytes_inflated
|
|
||||||
|
|
||||||
integer(pI64), dimension(:), allocatable :: temp, size_inflated, size_deflated
|
|
||||||
integer(pI64) :: headerLen, nBlock, b,s,e
|
|
||||||
|
|
||||||
|
|
||||||
if (headerType == 'UInt32') then
|
|
||||||
temp = int(prec_bytesToC_INT32_T(base64_to_bytes(base64_str(:base64_nChar(4_pI64)))),pI64)
|
|
||||||
nBlock = int(temp(1),pI64)
|
|
||||||
headerLen = 4_pI64 * (3_pI64 + nBlock)
|
|
||||||
temp = int(prec_bytesToC_INT32_T(base64_to_bytes(base64_str(:base64_nChar(headerLen)))),pI64)
|
|
||||||
else if (headerType == 'UInt64') then
|
|
||||||
temp = int(prec_bytesToC_INT64_T(base64_to_bytes(base64_str(:base64_nChar(8_pI64)))),pI64)
|
|
||||||
nBlock = int(temp(1),pI64)
|
|
||||||
headerLen = 8_pI64 * (3_pI64 + nBlock)
|
|
||||||
temp = int(prec_bytesToC_INT64_T(base64_to_bytes(base64_str(:base64_nChar(headerLen)))),pI64)
|
|
||||||
end if
|
|
||||||
|
|
||||||
allocate(size_inflated(nBlock),source=temp(2))
|
|
||||||
size_inflated(nBlock) = merge(temp(3),temp(2),temp(3)/=0_pI64)
|
|
||||||
size_deflated = temp(4:)
|
|
||||||
bytes_inflated = base64_to_bytes(base64_str(base64_nChar(headerLen)+1_pI64:))
|
|
||||||
|
|
||||||
allocate(bytes(sum(size_inflated)))
|
|
||||||
e = 0_pI64
|
|
||||||
do b = 1, nBlock
|
|
||||||
s = e + 1_pI64
|
|
||||||
e = s + size_deflated(b) - 1_pI64
|
|
||||||
bytes(sum(size_inflated(:b-1))+1_pI64:sum(size_inflated(:b))) = zlib_inflate(bytes_inflated(s:e),size_inflated(b))
|
|
||||||
end do
|
|
||||||
|
|
||||||
end function asBytes_compressed
|
|
||||||
|
|
||||||
|
|
||||||
!------------------------------------------------------------------------------------------------
|
|
||||||
!> @brief Interprete uncompressed Base64 string in vtk XML file as bytes
|
|
||||||
!> @details An uncompressed Base64 string consists of N headers blocks and a N data blocks
|
|
||||||
![#bytes-1/DATA-1][#bytes-2/DATA-2]...
|
|
||||||
!------------------------------------------------------------------------------------------------
|
|
||||||
function asBytes_uncompressed(base64_str,headerType) result(bytes)
|
|
||||||
|
|
||||||
character(len=*), intent(in) :: base64_str, & ! base64 encoded string
|
|
||||||
headerType ! header type (UInt32 or Uint64)
|
|
||||||
|
|
||||||
integer(pI64) :: s
|
|
||||||
integer(pI64), dimension(1) :: nByte
|
|
||||||
|
|
||||||
integer(C_SIGNED_CHAR), dimension(:), allocatable :: bytes
|
|
||||||
allocate(bytes(0))
|
|
||||||
|
|
||||||
s=0_pI64
|
|
||||||
if (headerType == 'UInt32') then
|
|
||||||
do while(s+base64_nChar(4_pI64)<(len(base64_str,pI64)))
|
|
||||||
nByte = int(prec_bytesToC_INT32_T(base64_to_bytes(base64_str(s+1_pI64:s+base64_nChar(4_pI64)))),pI64)
|
|
||||||
bytes = [bytes,base64_to_bytes(base64_str(s+1_pI64:s+base64_nChar(4_pI64+nByte(1))),5_pI64)]
|
|
||||||
s = s + base64_nChar(4_pI64+nByte(1))
|
|
||||||
end do
|
|
||||||
else if (headerType == 'UInt64') then
|
|
||||||
do while(s+base64_nChar(8_pI64)<(len(base64_str,pI64)))
|
|
||||||
nByte = int(prec_bytesToC_INT64_T(base64_to_bytes(base64_str(s+1_pI64:s+base64_nChar(8_pI64)))),pI64)
|
|
||||||
bytes = [bytes,base64_to_bytes(base64_str(s+1_pI64:s+base64_nChar(8_pI64+nByte(1))),9_pI64)]
|
|
||||||
s = s + base64_nChar(8_pI64+nByte(1))
|
|
||||||
end do
|
|
||||||
end if
|
|
||||||
|
|
||||||
end function asBytes_uncompressed
|
|
||||||
|
|
||||||
!------------------------------------------------------------------------------------------------
|
|
||||||
!> @brief Get XML string value for given key
|
|
||||||
!------------------------------------------------------------------------------------------------
|
|
||||||
pure function getXMLValue(line,key)
|
|
||||||
|
|
||||||
character(len=*), intent(in) :: line, key
|
|
||||||
|
|
||||||
character(len=:), allocatable :: getXMLValue
|
|
||||||
|
|
||||||
integer :: s,e
|
|
||||||
#ifdef __INTEL_COMPILER
|
|
||||||
character :: q
|
|
||||||
#endif
|
|
||||||
|
|
||||||
s = index(line," "//key,back=.true.)
|
|
||||||
if (s==0) then
|
|
||||||
getXMLValue = ''
|
|
||||||
else
|
|
||||||
e = s + 1 + scan(line(s+1:),"'"//'"')
|
|
||||||
if (scan(line(s:e-2),'=') == 0) then
|
|
||||||
getXMLValue = ''
|
|
||||||
else
|
|
||||||
s = e
|
|
||||||
! https://community.intel.com/t5/Intel-Fortran-Compiler/ICE-for-merge-with-strings/m-p/1207204#M151657
|
|
||||||
#ifdef __INTEL_COMPILER
|
|
||||||
q = line(s-1:s-1)
|
|
||||||
e = s + index(line(s:),q) - 1
|
|
||||||
#else
|
|
||||||
e = s + index(line(s:),merge("'",'"',line(s-1:s-1)=="'")) - 1
|
|
||||||
#endif
|
|
||||||
getXMLValue = line(s:e-1)
|
|
||||||
end if
|
|
||||||
end if
|
|
||||||
|
|
||||||
end function
|
|
||||||
|
|
||||||
|
|
||||||
!------------------------------------------------------------------------------------------------
|
|
||||||
!> @brief check for supported file format
|
|
||||||
!------------------------------------------------------------------------------------------------
|
|
||||||
pure function fileFormatOk(line)
|
|
||||||
|
|
||||||
character(len=*),intent(in) :: line
|
|
||||||
logical :: fileFormatOk
|
|
||||||
|
|
||||||
fileFormatOk = getXMLValue(line,'type') == 'ImageData' .and. &
|
|
||||||
getXMLValue(line,'byte_order') == 'LittleEndian' .and. &
|
|
||||||
getXMLValue(line,'compressor') /= 'vtkLZ4DataCompressor' .and. &
|
|
||||||
getXMLValue(line,'compressor') /= 'vtkLZMADataCompressor'
|
|
||||||
|
|
||||||
end function fileFormatOk
|
|
||||||
|
|
||||||
end subroutine readVTI
|
|
||||||
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
!---------------------------------------------------------------------------------------------------
|
||||||
!> @brief Calculate undeformed position of IPs/cell centers (pretend to be an element)
|
!> @brief Calculate undeformed position of IPs/cell centers (pretend to be an element)
|
||||||
!---------------------------------------------------------------------------------------------------
|
!---------------------------------------------------------------------------------------------------
|
||||||
|
|
|
||||||
Loading…
Reference in New Issue