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|
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
* terms governing use, modification, and redistribution, is contained in *
* the COPYING file, which can be found at the root of the source code *
* distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. *
* If you do not have access to either file, you may request a copy from *
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/****************/
/* Module Setup */
/****************/
#include "H5Dmodule.h" /* This source code file is part of the H5D module */
/***********/
/* Headers */
/***********/
#include "H5private.h" /* Generic Functions */
#include "H5CXprivate.h" /* API Contexts */
#include "H5Dpkg.h" /* Datasets */
#include "H5Eprivate.h" /* Error handling */
#include "H5FLprivate.h" /* Free lists */
#include "H5Iprivate.h" /* IDs */
/****************/
/* Local Macros */
/****************/
/******************/
/* Local Typedefs */
/******************/
/********************/
/* Local Prototypes */
/********************/
/*********************/
/* Package Variables */
/*********************/
/* Package initialization variable */
hbool_t H5_PKG_INIT_VAR = FALSE;
/* Declare extern the free list to manage blocks of VL data */
H5FL_BLK_EXTERN(vlen_vl_buf);
/* Declare extern the free list to manage other blocks of VL data */
H5FL_BLK_EXTERN(vlen_fl_buf);
/*****************************/
/* Library Private Variables */
/*****************************/
/* Declare extern the free list to manage blocks of type conversion data */
H5FL_BLK_EXTERN(type_conv);
/*******************/
/* Local Variables */
/*******************/
/*-------------------------------------------------------------------------
* Function: H5Dcreate2
*
* Purpose: Creates a new dataset named NAME at LOC_ID, opens the
* dataset for access, and associates with that dataset constant
* and initial persistent properties including the type of each
* datapoint as stored in the file (TYPE_ID), the size of the
* dataset (SPACE_ID), and other initial miscellaneous
* properties (DCPL_ID).
*
* All arguments are copied into the dataset, so the caller is
* allowed to derive new types, dataspaces, and creation
* parameters from the old ones and reuse them in calls to
* create other datasets.
*
* Return: Success: The object ID of the new dataset. At this
* point, the dataset is ready to receive its
* raw data. Attempting to read raw data from
* the dataset will probably return the fill
* value. The dataset should be closed when the
* caller is no longer interested in it.
*
* Failure: FAIL
*
* Programmer: Quincey Koziol
* Thursday, April 5, 2007
*
*-------------------------------------------------------------------------
*/
hid_t
H5Dcreate2(hid_t loc_id, const char *name, hid_t type_id, hid_t space_id,
hid_t lcpl_id, hid_t dcpl_id, hid_t dapl_id)
{
H5G_loc_t loc; /* Object location to insert dataset into */
H5D_t *dset = NULL; /* New dataset's info */
const H5S_t *space; /* Dataspace for dataset */
hid_t ret_value; /* Return value */
FUNC_ENTER_API(FAIL)
H5TRACE7("i", "i*siiiii", loc_id, name, type_id, space_id, lcpl_id, dcpl_id,
dapl_id);
/* Check arguments */
if(H5G_loc(loc_id, &loc) < 0)
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a location ID")
if(H5I_DATATYPE != H5I_get_type(type_id))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a datatype ID")
if(NULL == (space = (const H5S_t *)H5I_object_verify(space_id, H5I_DATASPACE)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataspace ID")
/* Get correct property list */
if(H5P_DEFAULT == lcpl_id)
lcpl_id = H5P_LINK_CREATE_DEFAULT;
else
if(TRUE != H5P_isa_class(lcpl_id, H5P_LINK_CREATE))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not link creation property list")
/* Get correct property list */
if(H5P_DEFAULT == dcpl_id)
dcpl_id = H5P_DATASET_CREATE_DEFAULT;
else
if(TRUE != H5P_isa_class(dcpl_id, H5P_DATASET_CREATE))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not dataset create property list ID")
/* Verify access property list and set up collective metadata if appropriate */
if(H5CX_set_apl(&dapl_id, H5P_CLS_DACC, loc_id, TRUE) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, H5I_INVALID_HID, "can't set access property list info")
/* Create the new dataset & get its ID */
if(NULL == (dset = H5D__create_named(&loc, name, type_id, space, lcpl_id, dcpl_id, dapl_id)))
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create dataset")
if((ret_value = H5I_register(H5I_DATASET, dset, TRUE)) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "unable to register dataset")
done:
if(ret_value < 0)
if(dset && H5D_close(dset) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release dataset")
FUNC_LEAVE_API(ret_value)
} /* end H5Dcreate2() */
/*-------------------------------------------------------------------------
* Function: H5Dcreate_anon
*
* Purpose: Creates a new dataset named NAME at LOC_ID, opens the
* dataset for access, and associates with that dataset constant
* and initial persistent properties including the type of each
* datapoint as stored in the file (TYPE_ID), the size of the
* dataset (SPACE_ID), and other initial miscellaneous
* properties (DCPL_ID).
*
* All arguments are copied into the dataset, so the caller is
* allowed to derive new types, dataspaces, and creation
* parameters from the old ones and reuse them in calls to
* create other datasets.
*
* The resulting ID should be linked into the file with
* H5Olink or it will be deleted when closed.
*
* Return: Success: The object ID of the new dataset. At this
* point, the dataset is ready to receive its
* raw data. Attempting to read raw data from
* the dataset will probably return the fill
* value. The dataset should be linked into
* the group hierarchy before being closed or
* it will be deleted. The dataset should be
* closed when the caller is no longer interested
* in it.
*
* Failure: FAIL
*
* Programmer: James Laird
* Tuesday, January 24, 2006
*
*-------------------------------------------------------------------------
*/
hid_t
H5Dcreate_anon(hid_t loc_id, hid_t type_id, hid_t space_id, hid_t dcpl_id,
hid_t dapl_id)
{
H5G_loc_t loc; /* Object location to insert dataset into */
H5D_t *dset = NULL; /* New dataset's info */
const H5S_t *space; /* Dataspace for dataset */
hid_t ret_value; /* Return value */
FUNC_ENTER_API(FAIL)
H5TRACE5("i", "iiiii", loc_id, type_id, space_id, dcpl_id, dapl_id);
/* Check arguments */
if(H5G_loc(loc_id, &loc) < 0)
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a location ID")
if(H5I_DATATYPE != H5I_get_type(type_id))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a datatype ID")
if(NULL == (space = (const H5S_t *)H5I_object_verify(space_id, H5I_DATASPACE)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataspace ID")
if(H5P_DEFAULT == dcpl_id)
dcpl_id = H5P_DATASET_CREATE_DEFAULT;
else
if(TRUE != H5P_isa_class(dcpl_id, H5P_DATASET_CREATE))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not dataset create property list ID")
/* Verify access property list and set up collective metadata if appropriate */
if(H5CX_set_apl(&dapl_id, H5P_CLS_DACC, loc_id, TRUE) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, H5I_INVALID_HID, "can't set access property list info")
/* build and open the new dataset */
if(NULL == (dset = H5D__create_anon(loc.oloc->file, type_id, space, dcpl_id, dapl_id)))
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create dataset")
/* Register the new dataset to get an ID for it */
if((ret_value = H5I_register(H5I_DATASET, dset, TRUE)) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "unable to register dataset")
done:
/* Release the dataset's object header, if it was created */
if(dset) {
H5O_loc_t *oloc; /* Object location for dataset */
/* Get the new dataset's object location */
if(NULL == (oloc = H5D_oloc(dset)))
HDONE_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to get object location of dataset")
/* Decrement refcount on dataset's object header in memory */
if(H5O_dec_rc_by_loc(oloc) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTDEC, FAIL, "unable to decrement refcount on newly created object")
} /* end if */
/* Cleanup on failure */
if(ret_value < 0)
if(dset && H5D_close(dset) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release dataset")
FUNC_LEAVE_API(ret_value)
} /* end H5Dcreate_anon() */
/*-------------------------------------------------------------------------
* Function: H5Dopen2
*
* Purpose: Finds a dataset named NAME at LOC_ID, opens it, and returns
* its ID. The dataset should be close when the caller is no
* longer interested in it.
*
* Takes a dataset access property list
*
* Return: Success: A new dataset ID
* Failure: FAIL
*
* Programmer: James Laird
* Thursday, July 27, 2006
*
*-------------------------------------------------------------------------
*/
hid_t
H5Dopen2(hid_t loc_id, const char *name, hid_t dapl_id)
{
H5D_t *dset = NULL;
H5G_loc_t loc; /* Object location of group */
hid_t ret_value;
FUNC_ENTER_API(FAIL)
H5TRACE3("i", "i*si", loc_id, name, dapl_id);
/* Check args */
if(H5G_loc(loc_id, &loc) < 0)
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a location")
if(!name || !*name)
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no name")
/* Verify access property list and set up collective metadata if appropriate */
if(H5CX_set_apl(&dapl_id, H5P_CLS_DACC, loc_id, FALSE) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, H5I_INVALID_HID, "can't set access property list info")
/* Open the dataset */
if(NULL == (dset = H5D__open_name(&loc, name, dapl_id)))
HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "unable to open dataset")
/* Register an atom for the dataset */
if((ret_value = H5I_register(H5I_DATASET, dset, TRUE)) < 0)
HGOTO_ERROR(H5E_ATOM, H5E_CANTREGISTER, FAIL, "can't register dataset atom")
done:
if(ret_value < 0)
if(dset && H5D_close(dset) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release dataset")
FUNC_LEAVE_API(ret_value)
} /* end H5Dopen2() */
/*-------------------------------------------------------------------------
* Function: H5Dclose
*
* Purpose: Closes access to a dataset (DATASET_ID) and releases
* resources used by it. It is illegal to subsequently use that
* same dataset ID in calls to other dataset functions.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Robb Matzke
* Thursday, December 4, 1997
*
*-------------------------------------------------------------------------
*/
herr_t
H5Dclose(hid_t dset_id)
{
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_API(FAIL)
H5TRACE1("e", "i", dset_id);
/* Check args */
if(NULL == H5I_object_verify(dset_id, H5I_DATASET))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset")
/*
* Decrement the counter on the dataset. It will be freed if the count
* reaches zero.
*/
if(H5I_dec_app_ref_always_close(dset_id) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTDEC, FAIL, "can't decrement count on dataset ID")
done:
FUNC_LEAVE_API(ret_value)
} /* end H5Dclose() */
/*-------------------------------------------------------------------------
* Function: H5Dget_space
*
* Purpose: Returns a copy of the file dataspace for a dataset.
*
* Return: Success: ID for a copy of the dataspace. The data
* space should be released by calling
* H5Sclose().
*
* Failure: FAIL
*
* Programmer: Robb Matzke
* Wednesday, January 28, 1998
*
*-------------------------------------------------------------------------
*/
hid_t
H5Dget_space(hid_t dset_id)
{
H5D_t *dset = NULL;
hid_t ret_value;
FUNC_ENTER_API(H5I_INVALID_HID)
H5TRACE1("i", "i", dset_id);
/* Check args */
if(NULL == (dset = (H5D_t *)H5I_object_verify(dset_id, H5I_DATASET)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, H5I_INVALID_HID, "not a dataset")
if((ret_value = H5D__get_space(dset)) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, H5I_INVALID_HID, "unable to get dataspace")
done:
FUNC_LEAVE_API(ret_value)
} /* end H5Dget_space() */
/*-------------------------------------------------------------------------
* Function: H5Dget_space_status
*
* Purpose: Returns the status of dataspace allocation.
*
* Return:
* Success: Non-negative
*
* Failture: Negative
*
* Programmer: Raymond Lu
*
*-------------------------------------------------------------------------
*/
herr_t
H5Dget_space_status(hid_t dset_id, H5D_space_status_t *allocation)
{
H5D_t *dset = NULL;
herr_t ret_value = SUCCEED;
FUNC_ENTER_API(FAIL)
H5TRACE2("e", "i*Ds", dset_id, allocation);
/* Check arguments */
if(NULL == (dset = (H5D_t *)H5I_object_verify(dset_id, H5I_DATASET)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset")
/* Read dataspace address and return */
if(H5D__get_space_status(dset, allocation) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to get space status")
done:
FUNC_LEAVE_API(ret_value)
} /* H5Dget_space_status() */
/*-------------------------------------------------------------------------
* Function: H5Dget_type
*
* Purpose: Returns a copy of the file datatype for a dataset.
*
* Return: Success: ID for a copy of the datatype. The data
* type should be released by calling
* H5Tclose().
*
* Failure: FAIL
*
* Programmer: Robb Matzke
* Tuesday, February 3, 1998
*
*-------------------------------------------------------------------------
*/
hid_t
H5Dget_type(hid_t dset_id)
{
H5D_t *dset; /* Dataset */
hid_t ret_value; /* Return value */
FUNC_ENTER_API(FAIL)
H5TRACE1("i", "i", dset_id);
/* Check args */
if(NULL == (dset = (H5D_t *)H5I_object_verify(dset_id, H5I_DATASET)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset")
if((ret_value = H5D__get_type(dset)) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to get dataspace")
done:
FUNC_LEAVE_API(ret_value)
} /* end H5Dget_type() */
/*-------------------------------------------------------------------------
* Function: H5Dget_create_plist
*
* Purpose: Returns a copy of the dataset creation property list.
*
* Return: Success: ID for a copy of the dataset creation
* property list. The template should be
* released by calling H5P_close().
*
* Failure: FAIL
*
* Programmer: Robb Matzke
* Tuesday, February 3, 1998
*
*-------------------------------------------------------------------------
*/
hid_t
H5Dget_create_plist(hid_t dset_id)
{
H5D_t *dataset; /* Dataset structure */
hid_t ret_value; /* Return value */
FUNC_ENTER_API(H5I_INVALID_HID)
H5TRACE1("i", "i", dset_id);
/* Check args */
if(NULL == (dataset = (H5D_t *)H5I_object_verify(dset_id, H5I_DATASET)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, H5I_INVALID_HID, "not a dataset")
if((ret_value = H5D__get_create_plist(dataset)) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, H5I_INVALID_HID, "Can't get creation plist")
done:
FUNC_LEAVE_API(ret_value)
} /* end H5Dget_create_plist() */
/*-------------------------------------------------------------------------
* Function: H5Dget_access_plist
*
* Purpose: Returns a copy of the dataset creation property list.
*
* Description: H5Dget_access_plist returns the dataset access property
* list identifier of the specified dataset.
*
* The chunk cache parameters in the returned property lists will be
* those used by the dataset. If the properties in the file access
* property list were used to determine the dataset’s chunk cache
* configuration, then those properties will be present in the
* returned dataset access property list. If the dataset does not
* use a chunked layout, then the chunk cache properties will be set
* to the default. The chunk cache properties in the returned list
* are considered to be “set”, and any use of this list will override
* the corresponding properties in the file’s file access property
* list.
*
* All link access properties in the returned list will be set to the
* default values.
*
* Return: Success: ID for a copy of the dataset access
* property list. The template should be
* released by calling H5Pclose().
*
* Failure: FAIL
*
* Programmer: Neil Fortner
* Wednesday, October 29, 2008
*
*-------------------------------------------------------------------------
*/
hid_t
H5Dget_access_plist(hid_t dset_id)
{
H5D_t *dset; /* Dataset structure */
hid_t ret_value; /* Return value */
FUNC_ENTER_API(FAIL)
H5TRACE1("i", "i", dset_id);
/* Check args */
if (NULL == (dset = (H5D_t *)H5I_object_verify(dset_id, H5I_DATASET)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset")
if((ret_value = H5D_get_access_plist(dset)) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "Can't get access plist")
done:
FUNC_LEAVE_API(ret_value)
} /* end H5Dget_access_plist() */
/*-------------------------------------------------------------------------
* Function: H5Dget_storage_size
*
* Purpose: Returns the amount of storage that is required for the
* dataset. For chunked datasets this is the number of allocated
* chunks times the chunk size.
*
* Return: Success: The amount of storage space allocated for the
* dataset, not counting meta data. The return
* value may be zero if no data has been stored.
*
* Failure: Zero
*
* Programmer: Robb Matzke
* Wednesday, April 21, 1999
*
*-------------------------------------------------------------------------
*/
hsize_t
H5Dget_storage_size(hid_t dset_id)
{
H5D_t *dset; /* Dataset to query */
hsize_t ret_value; /* Return value */
FUNC_ENTER_API(0)
H5TRACE1("h", "i", dset_id);
/* Check args */
if(NULL == (dset = (H5D_t *)H5I_object_verify(dset_id, H5I_DATASET)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, 0, "not a dataset")
/* Set return value */
if(H5D__get_storage_size(dset, &ret_value) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, 0, "can't get size of dataset's storage")
done:
FUNC_LEAVE_API(ret_value)
} /* end H5Dget_storage_size() */
/*-------------------------------------------------------------------------
* Function: H5Dget_offset
*
* Purpose: Returns the address of dataset in file.
*
* Return: Success: the address of dataset
*
* Failure: HADDR_UNDEF
*
* Programmer: Raymond Lu
* November 6, 2002
*
*-------------------------------------------------------------------------
*/
haddr_t
H5Dget_offset(hid_t dset_id)
{
H5D_t *dset; /* Dataset to query */
haddr_t ret_value; /* Return value */
FUNC_ENTER_API(HADDR_UNDEF)
H5TRACE1("a", "i", dset_id);
/* Check args */
if(NULL == (dset = (H5D_t *)H5I_object_verify(dset_id, H5I_DATASET)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, HADDR_UNDEF, "not a dataset")
/* Set return value */
ret_value = H5D__get_offset(dset);
done:
FUNC_LEAVE_API(ret_value)
} /* end H5Dget_offset() */
/*-------------------------------------------------------------------------
* Function: H5Diterate
*
* Purpose: This routine iterates over all the elements selected in a memory
* buffer. The callback function is called once for each element selected
* in the dataspace. The selection in the dataspace is modified so
* that any elements already iterated over are removed from the selection
* if the iteration is interrupted (by the H5D_operator_t function
* returning non-zero) in the "middle" of the iteration and may be
* re-started by the user where it left off.
*
* NOTE: Until "subtracting" elements from a selection is implemented,
* the selection is not modified.
*
* Parameters:
* void *buf; IN/OUT: Pointer to the buffer in memory containing
* the elements to iterate over.
* hid_t type_id; IN: Datatype ID for the elements stored in BUF.
* hid_t space_id; IN: Dataspace ID for BUF, also contains the
* selection to iterate over.
* H5D_operator_t op; IN: Function pointer to the routine to be
* called for each element in BUF iterated over.
* void *operator_data; IN/OUT: Pointer to any user-defined data
* associated with the operation.
*
* Operation information:
* H5D_operator_t is defined as:
* typedef herr_t (*H5D_operator_t)(void *elem, hid_t type_id,
* unsigned ndim, const hsize_t *point, void *operator_data);
*
* H5D_operator_t parameters:
* void *elem; IN/OUT: Pointer to the element in memory containing
* the current point.
* hid_t type_id; IN: Datatype ID for the elements stored in ELEM.
* unsigned ndim; IN: Number of dimensions for POINT array
* const hsize_t *point; IN: Array containing the location of the element
* within the original dataspace.
* void *operator_data; IN/OUT: Pointer to any user-defined data
* associated with the operation.
*
* The return values from an operator are:
* Zero causes the iterator to continue, returning zero when all
* elements have been processed.
* Positive causes the iterator to immediately return that positive
* value, indicating short-circuit success. The iterator can be
* restarted at the next element.
* Negative causes the iterator to immediately return that value,
* indicating failure. The iterator can be restarted at the next
* element.
*
* Return: Returns the return value of the last operator if it was non-zero,
* or zero if all elements were processed. Otherwise returns a
* negative value.
*
* Programmer: Quincey Koziol
* Friday, June 11, 1999
*
*-------------------------------------------------------------------------
*/
herr_t
H5Diterate(void *buf, hid_t type_id, hid_t space_id, H5D_operator_t op,
void *operator_data)
{
H5T_t *type; /* Datatype */
H5S_t *space; /* Dataspace for iteration */
H5S_sel_iter_op_t dset_op; /* Operator for iteration */
herr_t ret_value; /* Return value */
FUNC_ENTER_API(FAIL)
H5TRACE5("e", "*xiix*x", buf, type_id, space_id, op, operator_data);
/* Check args */
if(NULL == op)
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid operator")
if(NULL == buf)
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid buffer")
if(H5I_DATATYPE != H5I_get_type(type_id))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "invalid datatype")
if(NULL == (type = (H5T_t *)H5I_object_verify(type_id, H5I_DATATYPE)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not an valid base datatype")
if(NULL == (space = (H5S_t *)H5I_object_verify(space_id, H5I_DATASPACE)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "invalid dataspace")
if(!(H5S_has_extent(space)))
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "dataspace does not have extent set")
dset_op.op_type = H5S_SEL_ITER_OP_APP;
dset_op.u.app_op.op = op;
dset_op.u.app_op.type_id = type_id;
ret_value = H5S_select_iterate(buf, type, space, &dset_op, operator_data);
done:
FUNC_LEAVE_API(ret_value)
} /* end H5Diterate() */
/*-------------------------------------------------------------------------
* Function: H5Dvlen_reclaim
*
* Purpose: Frees the buffers allocated for storing variable-length data
* in memory. Only frees the VL data in the selection defined in the
* dataspace. The dataset transfer property list is required to find the
* correct allocation/free methods for the VL data in the buffer.
*
* Return: Non-negative on success, negative on failure
*
* Programmer: Quincey Koziol
* Thursday, June 10, 1999
*
*-------------------------------------------------------------------------
*/
herr_t
H5Dvlen_reclaim(hid_t type_id, hid_t space_id, hid_t dxpl_id, void *buf)
{
H5S_t *space; /* Dataspace for iteration */
herr_t ret_value; /* Return value */
FUNC_ENTER_API(FAIL)
H5TRACE4("e", "iii*x", type_id, space_id, dxpl_id, buf);
/* Check args */
if(H5I_DATATYPE != H5I_get_type(type_id) || buf == NULL)
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid argument")
if(NULL == (space = (H5S_t *)H5I_object_verify(space_id, H5I_DATASPACE)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "invalid dataspace")
if(!(H5S_has_extent(space)))
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "dataspace does not have extent set")
/* Get the default dataset transfer property list if the user didn't provide one */
if(H5P_DEFAULT == dxpl_id)
dxpl_id = H5P_DATASET_XFER_DEFAULT;
else
if(TRUE != H5P_isa_class(dxpl_id, H5P_DATASET_XFER))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms")
/* Set DXPL for operation */
H5CX_set_dxpl(dxpl_id);
/* Call internal routine */
ret_value = H5D_vlen_reclaim(type_id, space, buf);
done:
FUNC_LEAVE_API(ret_value)
} /* end H5Dvlen_reclaim() */
/*-------------------------------------------------------------------------
* Function: H5Dvlen_get_buf_size
*
* Purpose: This routine checks the number of bytes required to store the VL
* data from the dataset, using the space_id for the selection in the
* dataset on disk and the type_id for the memory representation of the
* VL data, in memory. The *size value is modified according to how many
* bytes are required to store the VL data in memory.
*
* Implementation: This routine actually performs the read with a custom
* memory manager which basically just counts the bytes requested and
* uses a temporary memory buffer (through the H5FL API) to make certain
* enough space is available to perform the read. Then the temporary
* buffer is released and the number of bytes allocated is returned.
* Kinda kludgy, but easier than the other method of trying to figure out
* the sizes without actually reading the data in... - QAK
*
* Return: Non-negative on success, negative on failure
*
* Programmer: Quincey Koziol
* Wednesday, August 11, 1999
*
*-------------------------------------------------------------------------
*/
herr_t
H5Dvlen_get_buf_size(hid_t dataset_id, hid_t type_id, hid_t space_id,
hsize_t *size)
{
H5D_vlen_bufsize_t vlen_bufsize = {0, 0, 0, 0, 0, 0};
H5D_t *dset; /* Dataset for operation */
H5S_t *fspace = NULL; /* Dataset's dataspace */
H5S_t *mspace = NULL; /* Memory dataspace */
char bogus; /* bogus value to pass to H5Diterate() */
H5S_t *space; /* Dataspace for iteration */
H5T_t *type; /* Datatype */
H5S_sel_iter_op_t dset_op; /* Operator for iteration */
herr_t ret_value; /* Return value */
FUNC_ENTER_API(FAIL)
H5TRACE4("e", "iii*h", dataset_id, type_id, space_id, size);
/* Check args */
if(H5I_DATASET != H5I_get_type(dataset_id) ||
H5I_DATATYPE != H5I_get_type(type_id) || size == NULL)
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid argument")
if(NULL == (dset = (H5D_t *)H5I_object(dataset_id)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset")
if(NULL == (type = (H5T_t *)H5I_object_verify(type_id, H5I_DATATYPE)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not an valid base datatype")
if(NULL == (space = (H5S_t *)H5I_object_verify(space_id, H5I_DATASPACE)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "invalid dataspace")
if(!(H5S_has_extent(space)))
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "dataspace does not have extent set")
/* Save the dataset */
vlen_bufsize.dset = dset;
/* Get a copy of the dataset's dataspace */
if(NULL == (fspace = H5S_copy(dset->shared->space, FALSE, TRUE)))
HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "unable to get dataspace")
vlen_bufsize.fspace = fspace;
/* Create a scalar for the memory dataspace */
if(NULL == (mspace = H5S_create(H5S_SCALAR)))
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCREATE, FAIL, "can't create dataspace")
vlen_bufsize.mspace = mspace;
/* Grab the temporary buffers required */
if(NULL == (vlen_bufsize.fl_tbuf = H5FL_BLK_MALLOC(vlen_fl_buf, (size_t)1)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "no temporary buffers available")
if(NULL == (vlen_bufsize.vl_tbuf = H5FL_BLK_MALLOC(vlen_vl_buf, (size_t)1)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "no temporary buffers available")
/* Set the memory manager to the special allocation routine */
if(H5CX_set_vlen_alloc_info(H5D__vlen_get_buf_size_alloc, &vlen_bufsize, NULL, NULL) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set VL data allocation routine")
/* Set the initial number of bytes required */
vlen_bufsize.size = 0;
/* Call H5S_select_iterate with args, etc. */
dset_op.op_type = H5S_SEL_ITER_OP_APP;
dset_op.u.app_op.op = H5D__vlen_get_buf_size;
dset_op.u.app_op.type_id = type_id;
ret_value = H5S_select_iterate(&bogus, type, space, &dset_op, &vlen_bufsize);
/* Get the size if we succeeded */
if(ret_value >= 0)
*size = vlen_bufsize.size;
done:
if(fspace && H5S_close(fspace) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release dataspace")
if(mspace && H5S_close(mspace) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release dataspace")
if(vlen_bufsize.fl_tbuf != NULL)
vlen_bufsize.fl_tbuf = H5FL_BLK_FREE(vlen_fl_buf, vlen_bufsize.fl_tbuf);
if(vlen_bufsize.vl_tbuf != NULL)
vlen_bufsize.vl_tbuf = H5FL_BLK_FREE(vlen_vl_buf, vlen_bufsize.vl_tbuf);
FUNC_LEAVE_API(ret_value)
} /* end H5Dvlen_get_buf_size() */
/*-------------------------------------------------------------------------
* Function: H5Dset_extent
*
* Purpose: Modifies the dimensions of a dataset.
* Can change to a smaller dimension.
*
* Return: Non-negative on success, negative on failure
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
* April 9, 2002
*
*-------------------------------------------------------------------------
*/
herr_t
H5Dset_extent(hid_t dset_id, const hsize_t size[])
{
H5D_t *dset; /* Dataset for this operation */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_API(FAIL)
H5TRACE2("e", "i*h", dset_id, size);
/* Check args */
if(NULL == (dset = (H5D_t *)H5I_object_verify(dset_id, H5I_DATASET)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset")
if(!size)
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no size specified")
/* Set up collective metadata if appropriate */
if(H5CX_set_loc(dset_id) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set collective metadata read info")
/* Private function */
if(H5D__set_extent(dset, size) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to set extend dataset")
done:
FUNC_LEAVE_API(ret_value)
} /* end H5Dset_extent() */
/*-------------------------------------------------------------------------
* Function: H5Dflush
*
* Purpose: Flushes all buffers associated with a dataset.
*
* Return: Non-negative on success, negative on failure
*
* Programmer: Mike McGreevy
* May 19, 2010
*
*-------------------------------------------------------------------------
*/
herr_t
H5Dflush(hid_t dset_id)
{
H5D_t *dset; /* Dataset for this operation */
herr_t ret_value = SUCCEED; /* return value */
FUNC_ENTER_API(FAIL)
H5TRACE1("e", "i", dset_id);
/* Check args */
if(NULL == (dset = (H5D_t *)H5I_object_verify(dset_id, H5I_DATASET)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset")
/* Set up collective metadata if appropriate */
if(H5CX_set_loc(dset_id) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set collective metadata read info")
/* Flush dataset information cached in memory */
if(H5D__flush(dset, dset_id) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTFLUSH, FAIL, "unable to flush cached dataset info")
done:
FUNC_LEAVE_API(ret_value)
} /* H5Dflush */
/*-------------------------------------------------------------------------
* Function: H5Drefresh
*
* Purpose: Refreshes all buffers associated with a dataset.
*
* Return: Non-negative on success, negative on failure
*
* Programmer: Mike McGreevy
* July 21, 2010
*
*-------------------------------------------------------------------------
*/
herr_t
H5Drefresh(hid_t dset_id)
{
H5D_t *dset; /* Dataset to refresh */
herr_t ret_value = SUCCEED; /* return value */
FUNC_ENTER_API(FAIL)
H5TRACE1("e", "i", dset_id);
/* Check args */
if(NULL == (dset = (H5D_t *)H5I_object_verify(dset_id, H5I_DATASET)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset")
/* Set up collective metadata if appropriate */
if(H5CX_set_loc(dset_id) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set collective metadata read info")
/* Call private function to refresh the dataset object */
if((H5D__refresh(dset_id, dset)) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTLOAD, FAIL, "unable to refresh dataset")
done:
FUNC_LEAVE_API(ret_value)
} /* end H5Drefresh() */
/*-------------------------------------------------------------------------
* Function: H5Dformat_convert (Internal)
*
* Purpose: For chunked:
* Convert the chunk indexing type to version 1 B-tree if not
* For compact/contiguous:
* Downgrade layout version to 3 if greater than 3
* For virtual: no conversion
*
* Return: Non-negative on success, negative on failure
*
* Programmer: Vailin Choi
* Feb 2015
*
*-------------------------------------------------------------------------
*/
herr_t
H5Dformat_convert(hid_t dset_id)
{
H5D_t *dset; /* Dataset to refresh */
herr_t ret_value = SUCCEED; /* return value */
FUNC_ENTER_API(FAIL)
H5TRACE1("e", "i", dset_id);
/* Check args */
if(NULL == (dset = (H5D_t *)H5I_object_verify(dset_id, H5I_DATASET)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset")
/* Set up collective metadata if appropriate */
if(H5CX_set_loc(dset_id) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set collective metadata read info")
switch(dset->shared->layout.type) {
case H5D_CHUNKED:
/* Convert the chunk indexing type to version 1 B-tree if not */
if(dset->shared->layout.u.chunk.idx_type != H5D_CHUNK_IDX_BTREE)
if((H5D__format_convert(dset)) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTLOAD, FAIL, "unable to downgrade chunk indexing type for dataset")
break;
case H5D_CONTIGUOUS:
case H5D_COMPACT:
/* Downgrade the layout version to 3 if greater than 3 */
if(dset->shared->layout.version > H5O_LAYOUT_VERSION_DEFAULT)
if((H5D__format_convert(dset)) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTLOAD, FAIL, "unable to downgrade layout version for dataset")
break;
case H5D_VIRTUAL:
/* Nothing to do even though layout is version 4 */
break;
case H5D_LAYOUT_ERROR:
case H5D_NLAYOUTS:
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "invalid dataset layout type")
default:
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "unknown dataset layout type")
} /* end switch */
done:
FUNC_LEAVE_API(ret_value)
} /* H5Dformat_convert */
/*-------------------------------------------------------------------------
* Function: H5Dget_chunk_index_type (Internal)
*
* Purpose: Retrieve a dataset's chunk indexing type
*
* Return: Non-negative on success, negative on failure
*
* Programmer: Vailin Choi
* Feb 2015
*
*-------------------------------------------------------------------------
*/
herr_t
H5Dget_chunk_index_type(hid_t did, H5D_chunk_index_t *idx_type)
{
H5D_t *dset; /* Dataset to refresh */
herr_t ret_value = SUCCEED; /* return value */
FUNC_ENTER_API(FAIL)
H5TRACE2("e", "i*Dk", did, idx_type);
/* Check args */
if(NULL == (dset = (H5D_t *)H5I_object_verify(did, H5I_DATASET)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset")
/* Should be a chunked dataset */
if(dset->shared->layout.type != H5D_CHUNKED)
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "dataset is not chunked")
/* Get the chunk indexing type */
if(idx_type)
*idx_type = dset->shared->layout.u.chunk.idx_type;
done:
FUNC_LEAVE_API(ret_value)
} /* H5Dget_chunk_index_type() */
/*-------------------------------------------------------------------------
* Function: H5Dget_chunk_storage_size
*
* Purpose: Returns the size of an allocated chunk.
*
* Return: Non-negative on success, negative on failure
*
* Programmer: Matthew Strong (GE Healthcare)
* 20 October 2016
*
*-------------------------------------------------------------------------
*/
herr_t
H5Dget_chunk_storage_size(hid_t dset_id, const hsize_t *offset, hsize_t *chunk_nbytes)
{
H5D_t *dset = NULL;
herr_t ret_value = SUCCEED;
FUNC_ENTER_API(FAIL)
H5TRACE3("e", "i*h*h", dset_id, offset, chunk_nbytes);
/* Check arguments */
if(NULL == (dset = (H5D_t *)H5I_object_verify(dset_id, H5I_DATASET)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset")
if( NULL == offset )
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid argument (null)")
if( NULL == chunk_nbytes )
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid argument (null)")
if(H5D_CHUNKED != dset->shared->layout.type)
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a chunked dataset")
/* Call private function */
if(H5D__get_chunk_storage_size(dset, offset, chunk_nbytes) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get storage size of chunk")
done:
FUNC_LEAVE_API(ret_value);
} /* H5Dget_chunk_storage_size() */
/*-------------------------------------------------------------------------
* Function: H5Dget_num_chunks
*
* Purpose: Retrieves the number of chunks that have nonempty intersection
* with a specified selection.
*
* Note: Currently, this function only gets the number of all written
* chunks, regardless the dataspace.
*
* Parameters:
* hid_t dset_id; IN: Chunked dataset ID
* hid_t fspace_id; IN: File dataspace ID
* hsize_t *nchunks; OUT:: Number of non-empty chunks
*
* Return: Non-negative on success, negative on failure
*
* Programmer: Binh-Minh Ribler
* August 2018 (EED-343)
*
*-------------------------------------------------------------------------
*/
herr_t
H5Dget_num_chunks(hid_t dset_id, hid_t fspace_id, hsize_t *nchunks)
{
H5D_t *dset = NULL;
const H5S_t *space; /* Dataspace for dataset */
herr_t ret_value = SUCCEED;
FUNC_ENTER_API(FAIL)
H5TRACE3("e", "ii*h", dset_id, fspace_id, nchunks);
/* Check arguments */
if(NULL == (dset = (H5D_t *)H5I_object_verify(dset_id, H5I_DATASET)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset")
if(NULL == (space = (const H5S_t *)H5I_object_verify(fspace_id, H5I_DATASPACE)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataspace ID")
if(NULL == nchunks)
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid argument (null)")
if(H5D_CHUNKED != dset->shared->layout.type)
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a chunked dataset")
/* Get the number of written chunks */
if(H5D__get_num_chunks(dset, space, nchunks) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error getting number of chunks")
done:
FUNC_LEAVE_API(ret_value);
} /* H5Dget_num_chunks() */
/*-------------------------------------------------------------------------
* Function: H5Dget_chunk_info
*
* Purpose: Retrieves information about a chunk specified by its index.
*
* Parameters:
* hid_t dset_id; IN: Chunked dataset ID
* hid_t fspace_id; IN: File dataspace ID
* hsize_t index; IN: Index of written chunk
* hsize_t *offset OUT: Offset coordinates of the chunk
* unsigned *filter_mask OUT: Filter mask
* haddr_t *addr OUT: Address of the chunk
* hsize_t *size OUT: Size of the chunk
*
* Return: Non-negative on success, negative on failure
*
* Programmer: Binh-Minh Ribler
* August 2018 (EED-343)
*
*-------------------------------------------------------------------------
*/
herr_t
H5Dget_chunk_info(hid_t dset_id, hid_t fspace_id, hsize_t index, hsize_t *offset, unsigned *filter_mask, haddr_t *addr, hsize_t *size)
{
H5D_t *dset = NULL;
const H5S_t *space; /* Dataspace for dataset */
hsize_t space_allocated = 0;
herr_t ret_value = SUCCEED;
FUNC_ENTER_API(FAIL)
H5TRACE7("e", "iih*h*Iu*a*h", dset_id, fspace_id, index, offset, filter_mask,
addr, size);
/* Check arguments */
if(NULL == (dset = (H5D_t *)H5I_object_verify(dset_id, H5I_DATASET)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset ID")
if(NULL == (space = (const H5S_t *)H5I_object_verify(fspace_id, H5I_DATASPACE)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataspace ID")
if(index < 0)
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid argument (null)")
if(NULL == offset && NULL == filter_mask && NULL == addr && NULL == size)
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid arguments, must have at least one non-null output argument")
if(H5D_CHUNKED != dset->shared->layout.type)
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a chunked dataset")
/* Call private function to get the chunk info given the chunk's index */
if(H5D__get_chunk_info(dset, space, index, offset, filter_mask, addr, size) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "Can't get chunk info")
done:
FUNC_LEAVE_API(ret_value);
} /* H5Dget_chunk_info() */
/*-------------------------------------------------------------------------
* Function: H5Dget_chunk_info_by_coord
*
* Purpose: Retrieves information about a chunk specified by its offset
* coordinates.
*
* Parameters:
* hid_t dset_id IN: Chunked dataset ID
* hsize_t *offset IN: Coordinates of the chunk
* unsigned *filter_mask OUT: Filter mask
* haddr_t *addr OUT: Address of the chunk
* hsize_t *size OUT: Size of the chunk
*
* Return: Non-negative on success, negative on failure
*
* Programmer: Binh-Minh Ribler
* August 2018 (EED-343)
*
*-------------------------------------------------------------------------
*/
herr_t
H5Dget_chunk_info_by_coord(hid_t dset_id, const hsize_t *offset, unsigned *filter_mask, haddr_t *addr, hsize_t *size)
{
H5D_t *dset = NULL;
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_API(FAIL)
H5TRACE5("e", "i*h*Iu*a*h", dset_id, offset, filter_mask, addr, size);
/* Check arguments */
if(NULL == (dset = (H5D_t *)H5I_object_verify(dset_id, H5I_DATASET)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset")
if(NULL == offset)
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid argument (null)")
if(NULL == filter_mask && NULL == addr && NULL == size)
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid arguments, must have at least one non-null output argument")
if(H5D_CHUNKED != dset->shared->layout.type)
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a chunked dataset")
/* Internal function to get the chunk info */
if (H5D__get_chunk_info_by_coord(dset, offset, filter_mask, addr, size) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read unprocessed chunk data")
done:
FUNC_LEAVE_API(ret_value)
} /* end H5Dget_chunk_info_by_coord() */
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