Commit upstream/2.24.1 - coda

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~~.gitignore~~ less more

0		*.o
1		*.lo
2		*.la
3		*.class
4		.deps
5		.dirstamp
6		.libs
7		stamp-*
8		/.indent.pro
9		/Makefile
10		/Makefile.in
11		/aclocal.m4
12		/ar-lib
13		/autom4te.cache/
14		/classnoinst.stamp
15		/coda.h
16		/codacheck
17		/codacmp
18		/codadd
19		/codadump
20		/codaeval
21		/codafind
22		/compile
23		/config.guess
24		/config.h
25		/config.h.in
26		/config.log
27		/config.status
28		/config.sub
29		/configure
30		/depcomp
31		/findtypedef
32		/findtypedef.c
33		/fortran/Makefile
34		/idl/coda_idl.dlm
35		/install-sh
36		/java/build.xml
37		/java/coda.jar
38		/java/doc/Doxyfile
39		/libcoda/coda-expr-parser.c
40		/libcoda/coda-expr-parser.h
41		/libcoda/coda-expr-tokenizer.c
42		/libcoda/doc/Doxyfile
43		/libtool
44		/ltmain.sh
45		/m4/depend.am
46		/m4/libtool.m4
47		/m4/ltoptions.m4
48		/m4/ltsugar.m4
49		/m4/ltversion.m4
50		/m4/lt~obsolete.m4
51		/missing
52		/py-compile
53		/ylwrap

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CHANGES less more

	0	2.24.1 2022-12-07
	1	~~~~~~~~~~~~~~~~~
	2
	3	* Fixed printing of coda.Record objects in Python interface (missing
	4	end-of-line and support for 0-dimensional arrays).
	5
	6	2.24 2022-05-18
	7	~~~~~~~~~~~~~~~
	8
	9	* Added significant speed improvements for recursive reads in Python interface.
	10
0	11	2.23.1 2022-02-18
1	12	~~~~~~~~~~~~~~~~~
2	13
3	14	* Improved performance in Python interface for some use cases.
4	15
5		* Fixed backward compatibility issu with new Python interface (coda.CodaError
	16	* Fixed backward compatibility issue with new Python interface (coda.CodaError
6	17	has been reintroduced as an alias for the new coda.Error exception class).
7	18
8	19	2.23 2021-12-17

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CMakeLists.txt less more

4	4
5	5	project(CODA)
6	6
7		set(VERSION 2.23.1)
	7	set(VERSION 2.24.1)
8	8	set(CODA_VERSION \"${VERSION}\")
9	9	set(CPACK_PACKAGE_VERSION ${VERSION})
10	10

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INSTALL less more

34	34	and all documentation and examples. For the IDL and MATLAB interfaces,
35	35	pre-built versions are included for IDL 8.3 and higher for Windows, and
36	36	MATLAB R2019b (v9.7) and higher for Windows. For the Python interface, a
37		pre-built version for Python 3.7 is included. For the Java interface, a
38		pre-built version for JDK 8 is included. All CODA interfaces have been
	37	pre-built version for Python 3.11 is included. For the Java interface, a
	38	pre-built version for JDK 11 is included. All CODA interfaces have been
39	39	compiled with HDF4 and HDF5 support built in.
40	40
41	41	If you do not have the CODA package you need, you can download it from the

57	57	- If you plan on using the Python interface you need Python version 2.7 or
58	58	higher and the Python 'numpy' and 'cffi' packages.
59	59
60		- If you plan on using the Java interface you need JDK/JRE version 8.
	60	- If you plan on using the Java interface you need JDK/JRE version 8 or
	61	higher.
61	62
62	63	- If you use Windows you will need to have the Microsoft Visual C++
63	64	Redistributable Packages for Visual Studio 2015 installed.

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README less more

0	0	Copyright (C) 2007-2022 S[&]T, The Netherlands
1	1
2		CODA 2.23.1 Release Notes
	2	CODA 2.24.1 Release Notes
3	3
4	4
5	5	CODA is the Common Data Access framework that allows reading of scientific data

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configure.ac less more

0	0	# autoconf file for CODA
1		AC_INIT([CODA],[2.23.1])
	1	AC_INIT([CODA],[2.24.1])
2	2	AC_CONFIG_AUX_DIR([.])
3	3	AM_INIT_AUTOMAKE(foreign subdir-objects 1.12 -Wall)
4	4

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11	11	<a class="qindex" href="annotated.html">Classes</a>
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14		<!-- Generated by Doxygen 1.9.2 -->
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15	15	</div><!-- top -->
16	16	<div class="header">
17	17	<div class="headertitle"><div class="title">Class List</div></div>

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17	17	<div class="headertitle"><div class="title">Class Index</div></div>

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17	17	<li class="navelem"><b>nl</b></li><li class="navelem"><b>stcorp</b></li><li class="navelem"><b>coda</b></li><li class="navelem"><a class="el" href="classnl_1_1stcorp_1_1coda_1_1_product.html">Product</a></li> </ul>

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16	16	<ul>
17	17	<li class="navelem"><b>nl</b></li><li class="navelem"><b>stcorp</b></li><li class="navelem"><b>coda</b></li><li class="navelem"><a class="el" href="classnl_1_1stcorp_1_1coda_1_1_product.html">Product</a></li> </ul>

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17	17	<li class="navelem"><b>nl</b></li><li class="navelem"><b>stcorp</b></li><li class="navelem"><b>coda</b></li><li class="navelem"><a class="el" href="classnl_1_1stcorp_1_1coda_1_1_type.html">Type</a></li> </ul>

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15	15	<div id="nav-path" class="navpath">
16	16	<ul>
17	17	<li class="navelem"><b>nl</b></li><li class="navelem"><b>stcorp</b></li><li class="navelem"><b>coda</b></li><li class="navelem"><a class="el" href="classnl_1_1stcorp_1_1coda_1_1_type.html">Type</a></li> </ul>

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16	16	<div class="contents">
17	17	<div class="textblock">Here is a list of all documented class members with links to the class documentation for each member:</div>

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17	17

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16	16	<div><div class="header">
17	17	<div class="headertitle"><div class="title">CODA Java Interface </div></div>

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17	17	<div class="headertitle"><div class="title">CODA C interface </div></div>

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242	242
243	243	<div class="fragment"><pre>
244	244	import os
245
246	245	os.putenv('CODA_DEFINITION', '<your codadef search path>')
247
248		# ...
249
250	246	import coda
251	247	</pre></div>
252	248

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matlab/coda-matlab-traverse.c less more

97	97	index[i] = (int)((int32_t *)data)[i];
98	98	break;
99	99	default:
100		mexErrMsgTxt("index parameter not of type double or int32");
	100	mexErrMsgTxt("Index parameter not of type double or int32");
101	101	break;
102	102	}
103	103	}

138	138
139	139	if (type_class != coda_array_class)
140	140	{
141		mexErrMsgTxt("Error in paramater");
	141	mexErrMsgTxt("Using numeric index for type that is not an array");
142	142	}
143	143
144	144	for (i = 0; i < length; i++)

192	192	{
193	193	if (coda_errno == CODA_ERROR_ARRAY_NUM_DIMS_MISMATCH)
194	194	{
195		mexPrintf("ERROR: array dimensions mismatch\n");
196		mexErrMsgTxt("Error in parameter");
	195	mexErrMsgTxt("Error in parameter (array dimensions mismatch)");
197	196	}
198	197	if (coda_errno == CODA_ERROR_ARRAY_OUT_OF_BOUNDS)
199	198	{
200		mexPrintf("ERROR: array index out of bounds\n");
201		mexErrMsgTxt("Error in parameter");
	199	mexErrMsgTxt("Error in parameter (array index out of bounds)");
202	200	}
203	201	coda_matlab_coda_error();
204	202	}

213	211	}
214	212	else
215	213	{
216		mexErrMsgTxt("Error in paramater");
	214	mexErrMsgTxt("Error in parameter (not a string or integer)");
217	215	}
218	216
219	217	if (name != NULL)

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python/__init__.py less more

811	811
812	812	elif isinstance(data, numpy.ndarray):
813	813	dim = data.shape
	814	if len(dim) == 0:
	815	dim = [1]
814	816	dimString = ""
815	817	for d in dim[:-1]:
816	818	dimString += "%ix" % (d,)
817	819	dimString += "%i" % (dim[-1],)
818		out.write("[%s %s]" % (dimString,self._typeToString[data.dtype.type]))
	820	out.write("[%s %s]" % (dimString, self._typeToString[data.dtype.type]))
819	821
820	822	elif _is_str(data):
821	823	out.write("\"%s\"" % (data,))

824	826	# if type is none of the above, fall back
825	827	# on the type specific __str__() function.
826	828	out.write("%s" % (data,))
	829
	830	out.write("\n")
827	831
828	832	return out.getvalue()
829	833

2381	2385	#
2382	2386	# PATH TRAVERSAL
2383	2387	#
2384		def _traverse_path(cursor, path, start=0):
	2388	def _traverse_path(cursor, path, start=0, type_path=None):
2385	2389	"""
2386	2390	_traverse_path() traverses the specified path until
2387	2391	an array with variable indices is encountered or the

2390	2394	thrown when a check fails.
2391	2395	"""
2392	2396
	2397	reldepth = 0
	2398
2393	2399	for pathIndex in range(start, len(path)):
	2400	if type_path is not None:
	2401	index = type_path[pathIndex]
	2402	if index is not None:
	2403	if _goto_index(cursor._x, index) != 0: # optimized to avoid lookup, boilerplate call
	2404	raise CodacError('coda_cursor_goto_record_field_by_index')
	2405	reldepth += 1
	2406	continue
	2407
2394	2408	if isinstance(path[pathIndex], str):
2395	2409	cursor_goto(cursor, path[pathIndex])
	2410	reldepth += 1
2396	2411	else:
2397	2412	if isinstance(path[pathIndex], int):
2398	2413	arrayIndex = [path[pathIndex]]

2428	2443	raise ValueError("array index (%i) exceeds array range [0:%i)" % (arrayIndex[i], arrayShape[i]))
2429	2444
2430	2445	if intermediateArray:
2431		return (True, pathIndex)
	2446	return (True, pathIndex, reldepth)
2432	2447	else:
2433	2448	# if all indices are non-variable, just move the cursor
2434	2449	# to the indicated element.

2436	2451	cursor_goto_array_element(cursor, [])
2437	2452	else:
2438	2453	cursor_goto_array_element(cursor, arrayIndex)
	2454	reldepth += 1
2439	2455
2440	2456	# we've arrived at the end of the path.
2441		return (False, len(path) - 1)
	2457	return (False, len(path) - 1, reldepth)
2442	2458
2443	2459
2444	2460	#
2445	2461	# HELPER FUNCTIONS FOR CODA.FETCH()
2446	2462	#
2447		def _fetch_intermediate_array(cursor, path, pathIndex=0): # TODO use type tree!
	2463	def _fetch_intermediate_array(cursor, path, pathIndex=0, type_path=None):
2448	2464	"""
2449	2465	_fetch_intermediate_array calls _traverse_path() to traverse the path
2450	2466	until the end is reached or an intermediate array is encountered.

2454	2470	recursively fetches each element of the array. note that this will result
2455	2471	in calls to _fetch_data().
2456	2472	"""
2457
2458	2473	arrayShape = cursor_get_array_dim(cursor)
2459	2474
2460	2475	# handle a rank-0 array by converting it to

2519	2534	for i in range(0, elementCount):
2520	2535	# move the cursor to the next required array element.
2521	2536	while currentElementIndex < nextElementIndex:
2522		cursor_goto_next_array_element(cursor)
	2537	if _goto_next_elem(cursor._x) != 0: # optimized to avoid lookup, boilerplate call
	2538	raise CodacError('coda_cursor_goto_next_array_element')
2523	2539	currentElementIndex += 1
2524	2540
2525		depth = cursor_get_depth(cursor)
2526
2527	2541	# traverse the path.
2528		(intermediateNode, copiedPathIndex) = _traverse_path(cursor, path, pathIndex + 1)
	2542	(intermediateNode, copiedPathIndex, reldepth) = _traverse_path(cursor, path, pathIndex + 1, type_path)
2529	2543
2530	2544	# create the result array by examining the type of the first element.
2531	2545	# This is equivalent to i == 0

2567	2581	array = numpy.empty(dtype=numpyType, shape=tmpShape)
2568	2582	else:
2569	2583	array = numpy.empty(dtype=object, shape=tmpShape)
	2584	flat = array.flat # optimization
	2585
2570	2586
2571	2587	# when this point is reached, a result array has been allocated
2572	2588	# and the flatArrayIter is set.

2574	2590	# result stored.
2575	2591	if intermediateNode:
2576	2592	# an intermediate array was encountered.
2577		array.flat[i] = _fetch_intermediate_array(cursor, path, copiedPathIndex)
	2593	flat[i] = _fetch_intermediate_array(cursor, path, copiedPathIndex, type_path)
2578	2594	else:
2579	2595	# the end of the path was reached. from this point on,
2580	2596	# the entire subtree is fetched.
2581	2597
2582	2598	if nodeReader is not None:
2583		array.flat[i] = nodeReader(cursor) # TODO optimize scalar leafs.. better yet, use type tree
	2599	flat[i] = nodeReader(cursor)
2584	2600	else:
2585		array.flat[i] = _fetch_subtree(cursor)
	2601	flat[i] = _fetch_subtree(cursor) # TODO add type tree for leafs to type path
2586	2602
2587	2603	# update fetchIndex and nextElementIndex.
2588	2604	for j in range(0, len(fetchShape)):

2595	2611	fetchIndex[j] = 0
2596	2612	nextElementIndex -= fetchStep[j + 1]
2597	2613
2598		for j in range(cursor_get_depth(cursor) - depth):
2599		cursor_goto_parent(cursor)
	2614	for j in range(reldepth):
	2615	if _goto_parent(cursor._x) != 0: # optimized to avoid lookup, boilerplate call
	2616	raise CodacError('coda_cursor_goto_parent')
2600	2617
2601	2618	cursor_goto_parent(cursor)
2602	2619	return array

2725	2742
2726	2743	elif class_ == CLASS_SPECIAL:
2727	2744	return type_tree[1](cursor)
	2745
	2746
	2747	# TODO we currently only cache field indices here, which helps a lot.
	2748	# TODO for small arrays, it would probably help to cache more information.
	2749	# TODO we probably also want to pre-determine the type tree for leafs.
	2750
	2751	def _determine_type_path(nodeType, path):
	2752	type_path = []
	2753	for segment in path:
	2754	if isinstance(segment, str):
	2755	i = type_get_record_field_index_from_name(nodeType, segment)
	2756	type_path.append(i)
	2757	nodeType = type_get_record_field_type(nodeType, i)
	2758	else:
	2759	type_path.append(None)
	2760	nodeType = type_get_array_base_type(nodeType)
	2761	return type_path
2728	2762
2729	2763
2730	2764	def _determine_type_tree(nodeType):

2829	2863
2830	2864	cursor = _get_cursor(start)
2831	2865
2832		(intermediateNode, pathIndex) = _traverse_path(cursor, path)
	2866	(intermediateNode, _, _) = _traverse_path(cursor, path)
2833	2867	if intermediateNode:
2834	2868	# we encountered an array with variable (-1) indices.
2835	2869	# this is only allowed when calling coda.fetch().

2860	2894
2861	2895	cursor = _get_cursor(start)
2862	2896
2863		(intermediateNode, pathIndex) = _traverse_path(cursor, path)
	2897	(intermediateNode, _, _) = _traverse_path(cursor, path)
2864	2898	if intermediateNode:
2865	2899	# we encountered an array with variable (-1) indices.
2866	2900	# this is only allowed when calling coda.fetch().

2907	2941	if _is_str(start):
2908	2942	product = start = Product(start)
2909	2943	cursor = _get_cursor(start)
	2944	nodeType = cursor_get_type(cursor)
2910	2945
2911	2946	# traverse the path
2912		(intermediateNode, pathIndex) = _traverse_path(cursor, path)
	2947	(intermediateNode, pathIndex, _) = _traverse_path(cursor, path)
2913	2948
2914	2949	try:
2915	2950	if (intermediateNode):
2916		result = _fetch_intermediate_array(cursor, path, pathIndex)
	2951	type_path = _determine_type_path(nodeType, path)
	2952	result = _fetch_intermediate_array(cursor, path, pathIndex, type_path)
2917	2953	else:
2918	2954	result = _fetch_subtree(cursor)
2919	2955	finally:

2948	2984	cursor = _get_cursor(start)
2949	2985
2950	2986	# traverse up until the last node of the path.
2951		(intermediateNode, pathIndex) = _traverse_path(cursor, path[:-1])
	2987	(intermediateNode, _, _) = _traverse_path(cursor, path[:-1])
2952	2988	if intermediateNode:
2953	2989	# we encountered an array with variable (-1) indices.
2954	2990	# this is only allowed when calling coda.fetch().

2983	3019
2984	3020	cursor = _get_cursor(start)
2985	3021
2986		(intermediateNode, pathIndex) = _traverse_path(cursor, path)
	3022	(intermediateNode, _, _) = _traverse_path(cursor, path)
2987	3023	if intermediateNode:
2988	3024	# we encountered an array with variable (-1) indices.
2989	3025	# this is only allowed when calling coda.fetch().

3022	3058
3023	3059	cursor = _get_cursor(start)
3024	3060
3025		(intermediateNode, pathIndex) = _traverse_path(cursor, path)
	3061	(intermediateNode, _, _) = _traverse_path(cursor, path)
3026	3062	if intermediateNode:
3027	3063	# we encountered an array with variable (-1) indices.
3028	3064	# this is only allowed when calling coda.fetch().

3064	3100
3065	3101	cursor = _get_cursor(start)
3066	3102
3067		(intermediateNode, pathIndex) = _traverse_path(cursor, path)
	3103	(intermediateNode, _, _) = _traverse_path(cursor, path)
3068	3104	if intermediateNode:
3069	3105	# we encountered an array with variable (-1) indices.
3070	3106	# this is only allowed when calling coda.fetch().

3145	3181
3146	3182	cursor = _get_cursor(start)
3147	3183
3148		(intermediateNode, pathIndex) = _traverse_path(cursor, path)
	3184	(intermediateNode, _, _) = _traverse_path(cursor, path)
3149	3185	if intermediateNode:
3150	3186	# we encountered an array with variable (-1) indices.
3151	3187	# this is only allowed when calling coda.fetch().

3173	3209
3174	3210	def _init():
3175	3211	"""Initialize the CODA Python interface."""
3176		global _lib, _encoding
	3212	global _lib, _encoding, _goto_index, _goto_parent, _goto_next_elem
3177	3213	# Initialize the CODA C library
3178	3214	clib = _get_c_library_filename()
3179	3215	_lib = _ffi.dlopen(clib)
	3216	_goto_index = _lib.coda_cursor_goto_record_field_by_index
	3217	_goto_parent = _lib.coda_cursor_goto_parent
	3218	_goto_next_elem = _lib.coda_cursor_goto_next_array_element
3180	3219
3181	3220	# Import constants
3182	3221	for attrname in dir(_lib):