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59e04ae071
cloud using a variant of the Zarr protocol and storage format. This enhancement is generically referred to as "NCZarr". The data model supported by NCZarr is netcdf-4 minus the user-defined types and the String type. In this sense it is similar to the CDF-5 data model. More detailed information about enabling and using NCZarr is described in the document NUG/nczarr.md and in a [Unidata Developer's blog entry](https://www.unidata.ucar.edu/blogs/developer/en/entry/overview-of-zarr-support-in). WARNING: this code has had limited testing, so do use this version for production work. Also, performance improvements are ongoing. Note especially the following platform matrix of successful tests: Platform | Build System | S3 support ------------------------------------ Linux+gcc | Automake | yes Linux+gcc | CMake | yes Visual Studio | CMake | no Additionally, and as a consequence of the addition of NCZarr, major changes have been made to the Filter API. NOTE: NCZarr does not yet support filters, but these changes are enablers for that support in the future. Note that it is possible (probable?) that there will be some accidental reversions if the changes here did not correctly mimic the existing filter testing. In any case, previously filter ids and parameters were of type unsigned int. In order to support the more general zarr filter model, this was all converted to char*. The old HDF5-specific, unsigned int operations are still supported but they are wrappers around the new, char* based nc_filterx_XXX functions. This entailed at least the following changes: 1. Added the files libdispatch/dfilterx.c and include/ncfilter.h 2. Some filterx utilities have been moved to libdispatch/daux.c 3. A new entry, "filter_actions" was added to the NCDispatch table and the version bumped. 4. An overly complex set of structs was created to support funnelling all of the filterx operations thru a single dispatch "filter_actions" entry. 5. Move common code to from libhdf5 to libsrc4 so that it is accessible to nczarr. Changes directly related to Zarr: 1. Modified CMakeList.txt and configure.ac to support both C and C++ -- this is in support of S3 support via the awd-sdk libraries. 2. Define a size64_t type to support nczarr. 3. More reworking of libdispatch/dinfermodel.c to support zarr and to regularize the structure of the fragments section of a URL. Changes not directly related to Zarr: 1. Make client-side filter registration be conditional, with default off. 2. Hack include/nc4internal.h to make some flags added by Ed be unique: e.g. NC_CREAT, NC_INDEF, etc. 3. cleanup include/nchttp.h and libdispatch/dhttp.c. 4. Misc. changes to support compiling under Visual Studio including: * Better testing under windows for dirent.h and opendir and closedir. 5. Misc. changes to the oc2 code to support various libcurl CURLOPT flags and to centralize error reporting. 6. By default, suppress the vlen tests that have unfixed memory leaks; add option to enable them. 7. Make part of the nc_test/test_byterange.sh test be contingent on remotetest.unidata.ucar.edu being accessible. Changes Left TO-DO: 1. fix provenance code, it is too HDF5 specific.
228 lines
7.1 KiB
C
228 lines
7.1 KiB
C
/*********************************************************************
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* Copyright 2018, UCAR/Unidata
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* See netcdf/COPYRIGHT file for copying and redistribution conditions.
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*********************************************************************/
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#include "zincludes.h"
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static int pcounter = 0;
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/* Forward */
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static int compute_intersection(const NCZSlice* slice, const size64_t chunklen, NCZChunkRange* range);
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/**************************************************/
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/* Goal:create a vector of chunk ranges: one for each slice in
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the top-level input. For each slice, compute the index (not
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absolute position) of the first chunk that intersects the slice
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and the index of the last chunk that intersects the slice.
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In practice, the count = last - first + 1 is stored instead of the last index.
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*/
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int
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NCZ_compute_chunk_ranges(
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int rank, /* variable rank */
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const NCZSlice* slices, /* the complete set of slices |slices| == R*/
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const size64_t* chunklen, /* the chunk length corresponding to the dimensions */
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NCZChunkRange* ncr)
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{
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int stat = NC_NOERR;
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int i;
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for(i=0;i<rank;i++) {
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if((stat = compute_intersection(&slices[i],chunklen[i],&ncr[i])))
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goto done;
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}
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done:
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return stat;
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}
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static int
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compute_intersection(
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const NCZSlice* slice,
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const size64_t chunklen,
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NCZChunkRange* range)
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{
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range->start = floordiv(slice->start, chunklen);
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range->stop = ceildiv(slice->stop, chunklen);
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return NC_NOERR;
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}
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/**
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Compute the projection of a slice as applied to n'th chunk.
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This is somewhat complex because for the first projection, the
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start is the slice start, but after that, we have to take into
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account that for a non-one stride, the start point in a
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projection may be offset by some value in the range of
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0..(slice.stride-1).
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*/
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int
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NCZ_compute_projections(size64_t dimlen, size64_t chunklen, size64_t chunkindex, const NCZSlice* slice, size_t n, NCZProjection* projections)
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{
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int stat = NC_NOERR;
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size64_t offset,count,avail;
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NCZProjection* projection;
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projection = &projections[n];
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projection->id = ++pcounter;
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projection->chunkindex = chunkindex;
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offset = chunklen * chunkindex; /* with respect to dimension (WRD) */
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/* Actual limit of the n'th touched chunk, taking
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dimlen and stride->stop into account. */
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projection->limit = (chunkindex + 1) * chunklen; /* WRD */
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if(projection->limit > dimlen) projection->limit = dimlen;
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if(projection->limit > slice->stop) projection->limit = slice->stop;
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/* Len is no. of touched indices along this dimension */
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projection->len = projection->limit - offset;
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if(n == 0) {
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/*initial case: original slice start is in 1st projection */
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projection->first = slice->start; /* WRD */
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} else { /* n > 0 */
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NCZProjection* prev = &projections[n-1];
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/* prevunused is the amount unused at end of the previous chunk.
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=> we need to skip (slice->stride-prevunused) in this chunk */
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/* Compute limit of previous chunk */
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size64_t prevunused = prev->limit - prev->last;
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projection->first = offset + (slice->stride - prevunused); /* WRD */
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}
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/* Compute number of places touched in this chunk */
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avail = projection->limit - projection->first; /*WRD*/
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count = ceildiv(avail, slice->stride);
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/* Last place to be touched */
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projection->last = projection->first + ((slice->stride * count) - 1); /*WRD*/
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/* Compute the slice relative to this chunk.
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Recall the possibility that start+stride >= projection->limit */
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projection->chunkslice.start = (projection->first - offset);
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projection->chunkslice.stop = projection->chunkslice.start + (slice->stride * count);
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//+1
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if(slice->stop > projection->limit) {
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projection->chunkslice.stop = projection->len;
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}
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projection->chunkslice.stride = slice->stride;
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projection->chunkslice.len = chunklen;
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/* compute the I/O position: the "location" in the memory
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array to read/write items */
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if(n == 0)
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projection->iopos = 0;
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else
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projection->iopos = ceildiv(offset - slice->start, slice->stride);
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/* And number of I/O items */
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projection->iocount = count;
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projection->memslice.start = projection->iopos;
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projection->memslice.stop = projection->memslice.start + projection->iocount;
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projection->memslice.stride = 1;
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#if 0
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projection->memslice.len = projection->memslice.stop;
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#else
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projection->memslice.len = dimlen;
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#endif
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return stat;
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}
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/* Goal:
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Create a vector of projections wrt a slice and a sequence of chunks.
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*/
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int
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NCZ_compute_per_slice_projections(
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int r, /* which dimension are we projecting? */
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const NCZSlice* slice, /* the slice for which projections are computed */
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const NCZChunkRange* range, /* range */
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size64_t dimlen, /* the dimension length for r'th dimension */
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size64_t chunklen, /* the chunk length corresponding to the dimension */
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NCZSliceProjections* slp)
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{
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int stat = NC_NOERR;
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size64_t index,slicecount;
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size_t n;
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/* Part fill the Slice Projections */
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slp->r = r;
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slp->range = *range;
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slp->count = range->stop - range->start;
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if((slp->projections = calloc(slp->count,sizeof(NCZProjection))) == NULL)
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{stat = NC_ENOMEM; goto done;}
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/* Compute the total number of output items defined by this slice
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(equivalent to count as used by nc_get_vars) */
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slicecount = ceildiv((slice->stop - slice->start), slice->stride);
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if(slicecount < 0) slicecount = 0;
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/* Iterate over each chunk that intersects slice to produce projection */
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for(n=0,index=range->start;index<range->stop;index++,n++) {
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if((stat = NCZ_compute_projections(dimlen, chunklen, index, slice, n, slp->projections)))
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goto done;
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}
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done:
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return stat;
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}
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/* Goal:create a vector of SliceProjection instances: one for each
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slice in the top-level input. For each slice, compute a set
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of projections from it wrt a dimension and a chunk size
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associated with that dimension.
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*/
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int
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NCZ_compute_all_slice_projections(
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int rank, /* variable rank */
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const NCZSlice* slices, /* the complete set of slices |slices| == R*/
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const size64_t* dimlen, /* the dimension lengths associated with a variable */
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const size64_t* chunklen, /* the chunk length corresponding to the dimensions */
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const NCZChunkRange* ranges,
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NCZSliceProjections* results)
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{
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int stat = NC_NOERR;
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size64_t r;
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for(r=0;r<rank;r++) {
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/* Compute each of the rank SliceProjections instances */
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NCZSliceProjections* slp = &results[r];
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if((stat=NCZ_compute_per_slice_projections(
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r,
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&slices[r],
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&ranges[r],
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dimlen[r],
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chunklen[r],
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slp))) goto done;
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}
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done:
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return stat;
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}
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/**************************************************/
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/* Utilities */
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void
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NCZ_clearsliceprojections(int count, NCZSliceProjections* slpv)
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{
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if(slpv != NULL) {
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int i;
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for(i=0;i<count;i++) {
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NCZSliceProjections* slp = &slpv[i];
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nullfree(slp->projections);
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}
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}
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}
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#if 0
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static void
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clearallprojections(NCZAllProjections* nap)
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{
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if(nap != NULL) {
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int i;
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for(i=0;i<nap->rank;i++)
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nclistfreeall(&nap->allprojections[i].projections);
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}
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}
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#endif
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