Filter: partial reading/writing of files
Preamble
This module provides services for partially reading or writing cgns files (HDF or ADF).
To use the module:
import Converter.Filter as Filter
List of functions
– Low level layer
Read a file and return a skeleton tree. |
|
Read nodes from file given their paths. |
|
Read nodes from file given a filter. |
|
Read nodes from file given their path and complete t. |
|
Write nodes to file given their paths. |
|
Write some nodes of the pyTree given their paths. |
|
Write nodes to file given a filter. |
|
|
Delete nodes in file given their paths. |
– High level layer
|
Handle for partial reading. |
Load a skeleton tree. |
|
|
Return the variable names contained in file. |
|
Fully load zones. |
Load zones without loading variables. |
|
Load specified variables. |
|
Write specified zones. |
|
Write specified zones without variables. |
|
Write specified variables. |
|
Load and distribute zones from proc node. |
|
Load and distribute zones. |
|
Load and split a file. |
Contents
Low level layer
-
Converter.Filter.
convertFile2SkeletonTree
(fileName, format=None, maxFloatSize=5, maxDepth=-1, links=None) Read a skeleton tree. If float data array size of DataArray_t type nodes is lower than maxFloatSize then the array is loaded. Otherwise it is set to None. If maxDepth is specified, load is limited to maxDepth levels.
- Parameters
fileName (string) – file name to read from
format (string) – bin_cgns, bin_adf, bin_hdf (optional)
maxFloatSize (int) – the maxSize of float array to load
maxDepth (int) – max depth of load
links (list of list of 4 strings) – if not None, return a list of links in file
- Returns
Skeleton tree
- Return type
pyTree node
For documentation on links, see Converter read options.
Example of use:
# - convertFile2SkeletonTree (pyTree) - import Converter.PyTree as C import Generator.PyTree as G import Converter.Filter as Filter import Converter.Internal as Internal a = G.cart((0.,0.,0.),(0.1,0.1,0.1),(11,11,11)) t = C.newPyTree(['Base', a]) C.convertPyTree2File(t, 'in.cgns') t = Filter.convertFile2SkeletonTree('in.cgns'); Internal.printTree(t) #>> ['CGNSTree',None,[2 sons],'CGNSTree_t'] #>> |_['CGNSLibraryVersion',array([3.0999999046325684],dtype='float64'),[0 son],'CGNSLibraryVersion_t'] #>> |_['Base',array(shape=(2,),dtype='int32',order='F'),[1 son],'CGNSBase_t'] #>> |_['cart',array(shape=(3, 3),dtype='int32',order='F'),[2 sons],'Zone_t'] #>> |_['ZoneType',array('Structured',dtype='|S1'),[0 son],'ZoneType_t'] #>> |_['GridCoordinates',None,[3 sons],'GridCoordinates_t'] #>> |_['CoordinateX',None,[0 son],'DataArray_t'] #>> |_['CoordinateY',None,[0 son],'DataArray_t'] #>> |_['CoordinateZ',None,[0 son],'DataArray_t']
-
Converter.Filter.
readNodesFromPaths
(fileName, paths, format=None, maxFloatSize=-1, maxDepth=-1, dataShape=None, skipTypes=None, com=None) Read nodes specified by their paths. If maxFloatSize=-1, all data are loaded, otherwise data are loaded only if the number of elements is lower that maxFloatSize. If maxDepth=-1, the read is fully recursive. Otherwise, load is limited to maxDepth levels. If skipTypes is specified, children of nodes of given type are not loaded (HDF only).
- Parameters
fileName (string) – file name to read from
paths (list of strings) – paths to read
format (string) – bin_cgns, bin_adf, bin_hdf (optional)
maxFloatSize (int) – the maxSize of float array to load
maxDepth (int) – max depth of load
dataShape (None or dictionary of shapes of data) – dictionary of returned data shapes if not None
skipTypes (None or list of strings) – list of CGNS types to skip
com (MPI communicator) – optional MPI communicator. If set, triggers parallel IO
- Returns
read nodes
- Return type
pyTree node list
Example of use:
# - readNodesFromPaths (pyTree) - import Converter.PyTree as C import Converter.Filter as Filter import Converter.Internal as Internal import Generator.PyTree as G # Cree le fichier test a = G.cart((0,0,0), (1,1,1), (10,10,10)) b = G.cart((12,0,0), (1,1,1), (10,10,10)) t = C.newPyTree(['Base',a,b]) C.convertPyTree2File(t, 'test.hdf') # Relit les noeuds par leur paths nodes = Filter.readNodesFromPaths('test.hdf', ['CGNSTree/Base/cart/GridCoordinates']) Internal.printTree(nodes) #>> ['GridCoordinates',None,[3 sons],'GridCoordinates_t'] #>> |_['CoordinateX',array(shape=(10, 10, 10),dtype='float64',order='F'),[0 son],'DataArray_t'] #>> |_['CoordinateY',array(shape=(10, 10, 10),dtype='float64',order='F'),[0 son],'DataArray_t'] #>> |_['CoordinateZ',array(shape=(10, 10, 10),dtype='float64',order='F'),[0 son],'DataArray_t']
-
Converter.Filter.
readNodesFromFilter
(fileName, filter, format='bin_hdf', com=None) Partially read nodes from a file specified by a filter. Filter is a dictionary for each path to be read. It specifies the slice of array you want to load from file and write to memory. Each slice information is made of [ offset, stride, count, block ]. Offset specifies the starting index of slice. Stride specifies the stride of slice (for example 1 means all elements, 2 means one over two, …). Count is the number of element to read. Block is always 1.
For example, for structured grids: [[imin,jmin,kmin], [1,1,1], [imax-imin+1,jmax-jmin+1,kmax-kmin+1], [1,1,1]].
For example, for unstructured grids: [[istart], [1], [iend-imax+1], [1]].
Only for HDFfile format.
- Parameters
fileName (string) – file name to read from
filter (dictionary of lists) – paths and indices to be read
format (string) – bin_hdf
com (MPI communicator) – optional MPI communicator. If set, tirggers parralel IO
- Returns
dictionary of read node data
- Return type
dictionary of numpys
Example of use:
# - readNodesFromFilter (pyTree) - import Converter.PyTree as C import Converter.Filter as Filter import Generator.PyTree as G # Cree le fichier test a = G.cart((0,0,0), (1,1,1), (10,10,10)) b = G.cart((12,0,0), (1,1,1), (10,10,10)) t = C.newPyTree(['Base',a,b]) C.convertPyTree2File(t, 'test.hdf') # Relit les noeuds par un filtre path = ['/Base/cart/GridCoordinates/CoordinateX', '/Base/cart/GridCoordinates/CoordinateY'] # start/stride/count (nbre d'entrees)/block # Read 2x2x2 data from file, starting from 1,1,1 DataSpaceMMRY = [[0,0,0], [1,1,1], [2,2,2], [1,1,1]] DataSpaceFILE = [[1,1,1], [1,1,1], [2,2,2], [1,1,1]] DataSpaceGLOB = [[10,10,10]] f = {} f[path[0]] = DataSpaceMMRY+DataSpaceFILE+DataSpaceGLOB f[path[1]] = DataSpaceMMRY+DataSpaceFILE+DataSpaceGLOB # Lit seulement les chemins fournis, retourne un dictionnaire des chemins lus a = Filter.readNodesFromFilter('test.hdf', f) print(a[path[0]]) #>> [1. 2. 1. 2. 1. 2. 1. 2.]
-
Converter.Filter.
readPyTreeFromPaths
(t, fileName, paths, format=None, maxFloatSize=-1, maxDepth=-1, dataShape=None, skipTypes=None, com=None) Read nodes of t specified by their paths. Exists also as in place function (_readPyTreeFromPaths) that modifies t and returns None.
- Parameters
t (pyTree) – input tree
fileName (string) – file name to read from
paths (list of strings) – paths to read
format (string) – bin_cgns, bin_adf, bin_hdf (optional)
maxFloatSize (int) – the maxSize of float array to load
maxDepth (int) – max depth of load
dataShape (None or dictionary of shapes of data) – dictionary of returned data shapes if not None
skipTypes (None or list of strings) – list of CGNS types to skip
com (MPI communicator) – optional MPI communicator. If set, triggers parallel IO
- Return type
modified tree
Example of use:
# - readPyTreeFromPaths (pyTree) - import Converter.PyTree as C import Converter.Filter as Filter import Generator.PyTree as G # Cree le fichier test a = G.cart((0,0,0), (1,1,1), (10,10,10)) b = G.cart((12,0,0), (1,1,1), (10,10,10)) t = C.newPyTree(['Base',a,b]) C.convertPyTree2File(t, 'test.hdf') t = Filter.convertFile2SkeletonTree('test.hdf', maxDepth=3) # Complete t par leur paths Filter._readPyTreeFromPaths(t, 'test.hdf', ['/Base/cart/GridCoordinates', 'Base/cart.0/GridCoordinates']) C.convertPyTree2File(t, 'out.hdf')
-
Converter.Filter.
writeNodesFromPaths
(fileName, paths, nodes, format=None, maxDepth=-1, mode=0) Write given nodes to specified paths in file. If mode=0 (append), nodes are appened to path location. Nevertheless, if a node with identical name already exists in the path node children, it will be replaced by the appended ones. If mode=1 (replace), nodes are replaced to path location. If maxDepth>0, replace mode kill children of replaced node. If maxDepth=0, replace mode replaces value and type of node (not the name).
- Parameters
fileName (string) – file name to write to
paths (list of strings) – paths to write to
nodes (list of pyTree nodes) – nodes to write
format (string) – bin_cgns, bin_adf, bin_hdf (optional)
maxDepth (int) – max depth to write
mode (int) – writing mode (0: append, 1: replace)
Example of use:
# - writeNodesFromPaths (pyTree) - import Generator.PyTree as G import Converter.PyTree as C import Converter.Filter as Filter t = C.newPyTree(['Base']) C.convertPyTree2File(t, 'out.hdf') # Append a = G.cart((0,0,0), (1,1,1), (10,10,10)) Filter.writeNodesFromPaths('out.hdf', 'CGNSTree/Base', a) # Append and replace a = G.cart((1,1,1), (1,1,1), (10,10,10)); a[0] = 'cart' Filter.writeNodesFromPaths('out.hdf', 'CGNSTree/Base', a)
-
Converter.Filter.
writePyTreeFromPaths
(t, fileName, paths, format=None, maxDepth=-1) Write given paths of tree to the same specified paths in file.
- Parameters
t (pyTree node) – input pyTree
fileName (string) – file name to write to
paths (list of strings) – paths to write to
format (string) – bin_cgns, bin_adf, bin_hdf (optional)
maxDepth (int) – max depth to write
Example of use:
# - writePyTreeFromPaths (pyTree) - import Generator.PyTree as G import Converter.PyTree as C import Converter.Filter as Filter t = C.newPyTree(['Base']) C.convertPyTree2File(t, 'out.hdf') a = G.cart((0,0,0), (1,1,1), (10,10,10)) t[2][1][2] += [a] Filter.writePyTreeFromPaths(t, 'out.hdf', 'CGNSTree/Base/cart')
-
Converter.Filter.
writePyTreeFromFilter
(t, fileName, filter, format='bin_hdf', com=None) Write partial data from tree t to file specified by a filter.
- Parameters
t (pyTree node) – input pyTree
fileName (string) – file name to write to
filter (dictionary of lists) – paths and indices to be read
format (string) – bin_cgns, bin_adf, bin_hdf (optional)
com (MPI communicator) – optional MPI communicator. If set, triggers parallel IO
Example of use:
# - writePyTreeFromFilter (pyTree) - import Generator.PyTree as G import Transform.PyTree as T import Converter.PyTree as C import Converter.Filter as Filter # Ecrit la zone en entier t = C.newPyTree(['Base']) a = G.cart((0,0,0), (1,1,1), (10,10,10)) t[2][1][2] += [a] C.convertPyTree2File(t, 'out.hdf') # Prend une subzone et la remplace dans le fichier t = C.newPyTree(['Base']) b = T.subzone(a, (2,2,2), (5,5,5)); b[0] = 'cart' C._initVars(b, 'CoordinateX', 1.) t[2][1][2] += [b] DataSpaceMMRY = [[0,0,0], [1,1,1], [4,4,4], [1,1,1]] DataSpaceFILE = [[2,2,2], [1,1,1], [4,4,4], [1,1,1]] DataSpaceGLOB = [[10,10,10]] f = {} f['/Base/cart/GridCoordinates/CoordinateX'] = DataSpaceMMRY+DataSpaceFILE+DataSpaceGLOB # skelData != None since node already exists Filter.writePyTreeFromFilter(t, 'out.hdf', f, skelData=[])
-
Converter.Filter.
deletePaths
(fileName, paths, format=None) Delete paths in file.
- Parameters
fileName (string) – file name to read from
paths (list of strings) – paths to read (relative to a)
format (string) – bin_cgns, bin_adf, bin_hdf (optional)
Example of use:
# - deletePaths (pyTree) - import Converter.PyTree as C import Converter.Filter as Filter t = C.newPyTree(['Base']) C.convertPyTree2File(t, 'out.hdf') # Delete paths Filter.deletePaths('out.hdf', 'CGNSTree/Base')
High level layer
-
Converter.Filter.
Handle
(fileName) Create a handle on a file to enable partial reading. The file must be a CGNS/ADF or CGNS/HDF file.
- Parameters
fileName (string) – file name to read from
- Return type
handle class
Example of use:
# - Filter.Handle - import Converter.Filter as Filter # Create a handle on a CGNS file h = Filter.Handle('file.hdf')
-
Converter.Filter.Handle.
loadSkeleton
(maxDepth=3, readProcNode=False) Load a skeleton tree from file (a tree of depth maxDepth where no data are loaded).
- Parameters
maxDepth (int) – the depth you want to load (-1 means all tree)
readProcNode (boolean) – if true, force reading of proc node. Usefull for maxDepth <= 4.
- Return type
a skeleton pyTree
Example of use:
# - loadSkeleton - import Converter.Filter as Filter import Converter.PyTree as C import Generator.PyTree as G # Create test case a = G.cart((0,0,0), (1,1,1), (10,10,10)) C.convertPyTree2File(a, 'file.hdf') # Create a handle on a CGNS file h = Filter.Handle('file.hdf') # Load skeleton a = h.loadSkeleton()
-
Converter.Filter.Handle.
getVariables
(cont=None) Get the names of variables contained in file. This function must be called after loadSkeleton.
- Parameters
cont – container name. Can be a CGNS name ‘FlowSolution’, … or ‘centers’ or ‘nodes’
- Returns
list of variable names contained in file
- Return type
list of strings
Example of use:
# - getVariables (pyTree) - import Converter.Filter as Filter import Converter.PyTree as C import Generator.PyTree as G # Create test case a = G.cart((0,0,0), (1,1,1), (10,10,10)) C._initVars(a, 'F', 0) C._initVars(a, 'centers:G', 1) C.convertPyTree2File(a, 'file.hdf') # Create a handle on a CGNS file h = Filter.Handle('file.hdf') # Load skeleton a = h.loadSkeleton() # Get variables from file vars = h.getVariables(); print(vars) #>> ['FlowSolution/F', 'FlowSolution#Centers/G']
-
Converter.Filter.Handle.
loadZones
(a, znp=None) Fully load specified zones (coordinates, fields, grid connectivity, boundary conditions) in tree. This function must be called after loadSkeleton.
- Parameters
a (pyTree) – modified pyTree
znp (list of strings) – paths of zones to load (must be a list of ‘BaseName/ZoneName’)
Example of use:
# - loadZonesVars (pyTree) - import Converter.Filter as Filter import Converter.PyTree as C import Generator.PyTree as G # Create test case a = G.cart((0,0,0), (1,1,1), (10,10,10)) b = G.cart((10,0,0), (1,1,1), (10,10,10)) C.convertPyTree2File([a,b], 'file.hdf') # Create a handle on a CGNS file h = Filter.Handle('file.hdf') # Load skeleton a = h.loadSkeleton() # Fully load all zones h._loadZones(a) # Fully load two zones h._loadZones(a, znp=['Base/cart', 'Base/cart.0'])
-
Converter.Filter.Handle.
loadZonesWoVars
(a, znp=None, bbox=None) Load specified zones (coordinates, grid connectivity, boundary conditions) in tree. If bbox=[xmin,ymin,zmin,xmax,ymax,zmax] is specified, load only zones intersecting this bbox. This function must be called after loadSkeleton.
- Parameters
a (pyTree) – modified pyTree
znp (list of strings) – path of zones to load from (starting from top)
bbox (list of 6 floats) – optional bbox
Example of use:
# - loadZonesWoVars (pyTree) - import Converter.Filter as Filter import Converter.PyTree as C import Generator.PyTree as G # Create test case a = G.cart((0,0,0), (1,1,1), (10,10,10)) C.convertPyTree2File(a, 'file.hdf') # Create a handle on a CGNS file h = Filter.Handle('file.hdf') # Load skeleton a = h.loadSkeleton() # Load all zones without variable h._loadZonesWoVars(a) # Load one zone without variable h._loadZonesWoVars(a, znp=['Base/cart'])
-
Converter.Filter.Handle.
loadVariables
(a, var, znp=None) Load specified variables in tree. This function must be called after loadSkeleton.
- Parameters
a (pyTree) – modified pyTree
var (string or list of strings) – variables to load
znp (list of strings) – path of zones to load from (starting from top)
Example of use:
# - loadVariables (pyTree) - import Converter.Filter as Filter import Converter.PyTree as C import Generator.PyTree as G # Create test case a = G.cart((0,0,0), (1,1,1), (10,10,10)) C._initVars(a, 'F', 0) C._initVars(a, 'centers:G', 1) C.convertPyTree2File(a, 'file.hdf') # Create a handle on a CGNS file h = Filter.Handle('file.hdf') # Load skeleton a = h.loadSkeleton() # Load all zones without variable h._loadZonesWoVars(a) # Load given variables for all zones h._loadVariables(a, var=['F', 'centers:G']) # Load given variables for given zone h._loadVariables(a, var=['F', 'centers:G'], znp=['Base/cart'])
-
Converter.Filter.Handle.
writeZones
(a, fileName=None, znp=None) Fully write specified zones (coordinates, fields, grid connectivity, boundary conditions) in file.
- Parameters
a (pyTree or list of zones) – input pyTree
fileName (string) – file name if different of handle name
znp (list of strings) – path of zones to write to in file (starting from root)
Example of use:
# - writeZones (pyTree) - # with Filter import Converter.PyTree as C import Generator.PyTree as G import Converter.Filter as Filter a = G.cart((0,0,0), (1,1,1), (10,10,10)) C._initVars(a, 'centers:Density=1.') b = G.cart((11,0,0), (1,1,1), (10,10,10)) C._initVars(b, 'centers:Density=1.') t = C.newPyTree(['Base']) C.convertPyTree2File(t, 'out.hdf') h = Filter.Handle('out.hdf') # Interface sur arbre (mais a doit etre mis dans t) t[2][1][2] = [a,b] h.writeZones(t, znp='Base/cart') # Interface sur zones h.writeZones(a, znp='Base/cart') h.writeZones([a,b], znp=['Base/cart','Base/cart.0'])
-
Converter.Filter.Handle.
writeZonesWoVars
(a, fileName=None, znp=None) Write specified zones without fields (coordinates, grid connectivity, boundary conditions) in file.
- Parameters
a (pyTree or list of zones) – input pyTree
fileName (string) – file name if different of handle name
znp (list of strings) – path of zones to write to in file (starting from root)
Example of use:
# - writeZones (pyTree) - # with Filter import Converter.PyTree as C import Generator.PyTree as G import Converter.Filter as Filter a = G.cart((0,0,0), (1,1,1), (10,10,10)) C._initVars(a, 'centers:Density=1.') b = G.cart((11,0,0), (1,1,1), (10,10,10)) C._initVars(b, 'centers:Density=1.') t = C.newPyTree(['Base']) C.convertPyTree2File(t, 'out.hdf') h = Filter.Handle('out.hdf') h.writeZonesWoVars(a, znp='Base/cart') h.writeZonesWoVars([a,b], znp=['Base/cart','Base/cart.0'])
-
Converter.Filter.Handle.
writeVariables
(a, var, fileName=None, znp=None) Write specified variables in file.
- Parameters
a (pyTree or list of zones) – input pyTree
var (string or list of strings) – variables to write
fileName (string) – file name if different of handle name
znp (list of strings) – path of zones to write to in file (starting from root)
Example of use:
# - writeVariables (pyTree) - # with Filter import Converter.PyTree as C import Generator.PyTree as G import Converter.Filter as Filter a = G.cart((0,0,0), (1,1,1), (10,10,10)) C._initVars(a, 'centers:Density=1.') b = G.cart((11,0,0), (1,1,1), (10,10,10)) C._initVars(b, 'centers:Density=1.') t = C.newPyTree(['Base']) C.convertPyTree2File(t, 'out.hdf') h = Filter.Handle('out.hdf') h.writeZonesWoVars(a, znp='Base/cart') h.writeVariables(a, 'centers:Density', znp='Base/cart')
-
Converter.Filter.Handle.
loadFromProc
(loadVariables=True) Load on each processor the zones with the corresponding proc node. The zones in file must have a .Solver#Param/proc node.
- Parameters
loadVariables (Boolean) – If true, load all variables in file. Otherwise load only coordinates
- Return type
partial tree on each processor
Example of use:
# - loadFromProc (pyTree) - import Converter.Filter as Filter import Converter.Internal as Internal import Converter.Mpi as Cmpi # Build case if Cmpi.rank == 0: import Converter.PyTree as C import Generator.PyTree as G import Transform.PyTree as T import Distributor2.PyTree as D2 a = G.cart((0,0,0), (1,1,1), (100,50,50)) a = T.splitNParts(a, Cmpi.size) D2._distribute(a, Cmpi.size) C.convertPyTree2File(a, 'case1.cgns') Cmpi.barrier() h = Filter.Handle('case1.cgns') a = h.loadFromProc() Internal.printTree(a) Cmpi.convertPyTree2File(a, 'out.cgns')
-
Converter.Filter.Handle.
loadAndDistribute
(strategy=None, algorithm='graph', loadVariables=True) Load and distribute zones of file on the different processors.
- Parameters
strategy (string) – strategy for distribution. Can be None (only the number of points of block is considered), ‘match’ (use matching boundaries to optimize distribution)
algorithm (string) – algorithm for distribution. Can be ‘graph’, ‘fast’, ‘gradient’. See Distributor2 documentation.
loadVariables (Boolean) – If true, load all variables in file. Otherwise load only coordinates
- Return type
partial tree on each processor
Example of use:
# - loadAndDistribute (pyTree) - import Converter.Filter as Filter import Converter.Internal as Internal import Converter.Mpi as Cmpi # Build case if Cmpi.rank == 0: import Converter.PyTree as C import Generator.PyTree as G import Transform.PyTree as T a = G.cart((0,0,0), (1,1,1), (100,50,50)) a = T.splitNParts(a, Cmpi.size) C.convertPyTree2File(a, 'case1.cgns') Cmpi.barrier() h = Filter.Handle('case1.cgns') a = h.loadAndDistribute() Internal.printTree(a) Cmpi.convertPyTree2File(a, 'out.cgns')
-
Converter.Filter.Handle.
loadAndSplit
() Load and split zones of file on the different processors (only for structured zones).
- Return type
partial tree on each processor
Example of use:
# - loadAndSplit (pyTree) - import Generator.PyTree as G import Converter.PyTree as C import Converter.Filter as Filter import Converter.Mpi as Cmpi # Build case if Cmpi.rank == 0: a = G.cart((0,0,0), (1,1,1), (100,100,100)) C.convertPyTree2File(a, 'out.hdf') Cmpi.barrier() # With skeleton h = Filter.Handle('out.hdf') t = h.loadAndSplitSkeleton(NParts=3) h._loadContainerPartial(t, variablesN=['GridCoordinates/CoordinateX','GridCoordinates/CoordinateY','GridCoordinates/CoordinateZ']) Cmpi.convertPyTree2File(t, 'out.cgns') # In one go h = Filter.Handle('out.hdf') t = h.loadAndSplit(NParts=3) Cmpi.convertPyTree2File(t, 'out.cgns')