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

Converter.Filter.convertFile2SkeletonTree(…)	Read a file and return a skeleton tree.
Converter.Filter.readNodesFromPaths(…[, …])	Read nodes from file given their paths.
Converter.Filter.readNodesFromFilter(…[, …])	Read nodes from file given a filter.
Converter.Filter.readPyTreeFromPaths(t, …)	Read nodes from file given their path and complete t.
Converter.Filter.writeNodesFromPaths(…[, …])	Write nodes to file given their paths.
Converter.Filter.deletePaths(fileName, paths)	Delete nodes in file given their paths.

– High level layer

Converter.Filter.Handle(fileName)	Handle for partial reading.
Converter.Filter.Handle.loadSkeleton()	Load a skeleton tree.
Converter.Filter.Handle.getVariables([a, cont])	Return the variable names contained in file.
Converter.Filter.Handle.loadZonesWoVars(a[, …])	Load zones without loading variables.
Converter.Filter.Handle.loadVariables(a, var)	Load specified variables.

Contents

Low level layer

Converter.Filter.convertFile2SkeletonTree(fileName, format=None, maxFloatSize=5, maxDepth=-1)

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

Returns:

Skeleton tree

Return type:

pyTree node

Example of use:

• Read skeleton tree (pyTree):

# - convertFile2SkeletonTree (pyTree) -
import Converter.PyTree as C
import Generator.PyTree as G
import Converter.Mpi as Cmpi
import Converter.Internal as Internal

if Cmpi.rank == 0:
    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')
Cmpi.barrier()

t1 = Cmpi.convertFile2SkeletonTree('in.cgns'); Internal.printTree(t1)
#>> ['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)

Read nodes specified by their paths.

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

Returns:

read nodes

Return type:

pyTree node list

Example of use:

• Read nodes from file (pyTree):

# - 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)

---

Converter.Filter.readNodesFromFilter(fileName, filter, format='bin_hdf', com=None)

Partially read nodes specified by a filter. Filter is a dictionary for each path to be read. For structured grids: [[imin,jmin,kmin], [1,1,1], [imax,jmax,kmax], [1,1,1]] For unstructured grids: [[istart], [1], [iend], [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 (int) – communicator if run with mpi

Returns:

dictionary of read nodes

Return type:

dictionary of numpys

Example of use:

• Partially read nodes from file (pyTree):

# - 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
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 = [[0]]

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]].ravel('k')

---

Converter.Filter.readPyTreeFromPaths(t, fileName, paths, format=None, maxFloatSize=-1, maxDepth=-1)

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

Return type:

modified tree

Example of use:

• Read nodes from file and modify tree (pyTree):

# - readPyTreeFromPaths (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')

t = Filter.convertFile2SkeletonTree('test.hdf', maxDepth=3)

# Complete t par leur paths
Filter._readPyTreeFromPaths(t, 'test.hdf', ['/Base/cart/GridCoordinates', 'Base/cart.0/GridCoordinates'])
Internal.printTree(t)
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. 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:

• Write nodes from paths (pyTree):

# - 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._readPyTreeFromPaths(a, fileName, paths, format=None, maxFloatSize=-1, maxDepth=-1)

Read nodes specified by their paths and stored it in a (in place).

Parameters:

• a ([pyTree, base, Zone, list of Zones]) – input data
• 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)
• maxFloatSize (int) – the maxSize of float array to load
• maxDepth (int) – max depth of load

Example of use:

• Read nodes from file and modify pyTree (pyTree):

# - readPyTreeFromPaths (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')

t = Filter.convertFile2SkeletonTree('test.hdf', maxDepth=3)

# Complete t par leur paths
Filter._readPyTreeFromPaths(t, 'test.hdf', ['/Base/cart/GridCoordinates', 'Base/cart.0/GridCoordinates'])
Internal.printTree(t)
C.convertPyTree2File(t, 'out.hdf')

---

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:

• Delete some nodes in file from paths (pyTree):

# - 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:

• Create a handle on a file (pyTree):

# - Filter.Handle -
import Converter.Filter as Filter

# Create a handle on a CGNS file
h = Filter.Handle('file.hdf')

---

Converter.Filter.Handle.loadSkeleton()

Load a skeleton tree from file (a tree where no data are loaded).

Return type:a skeleton pyTree

Example of use:

• Load a skeleton tree from file (pyTree):

# - 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()

Get the variables contained in file. This function minimal reads from file and store variable names in handle. This function must be called after loadSkeleton.

Returns:list of variables contained in file Return type:list of strings

Example of use:

• Read variable list from file (pyTree):

# - 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.loadZonesWoVars(a, znp=None, bbox=None)

Load specified zones (coordinates, grid connectivity, boundary conditions). 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:

• Load zones without variable (pyTree):

# - 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 zones without variable
h._loadZonesWoVars(a)

---

Converter.Filter.Handle.loadVariables(a, var, znp=None)

Load specified variables. 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:

• Load given variables (pyTree):

# - 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 zones without variable
h._loadZonesWoVars(a)

# Load given variables
h._loadVariables(a, var=['F', 'centers:G'])

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