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Merge pull request #11 from tboudreaux/docs/opatio

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aded docs to utils/opatio python module
This commit is contained in:
Emily Boudreaux
2025-02-16 12:49:53 -05:00
committed by GitHub
parent 5ce365d545 fde561cdef
commit c68d36fb55
52 changed files with 1201 additions and 388 deletions
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6
Doxyfile
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@@ -349,7 +349,7 @@ OPTIMIZE_OUTPUT_SLICE = NO
#
# Note see also the list of default file extension mappings.
EXTENSION_MAPPING =
EXTENSION_MAPPING = py=C++
# If the MARKDOWN_SUPPORT tag is enabled then Doxygen pre-processes all comments
# according to the Markdown format, which allows for more readable
@@ -534,7 +534,7 @@ TIMESTAMP = NO
# normally produced when WARNINGS is set to YES.
# The default value is: NO.
EXTRACT_ALL = NO
EXTRACT_ALL = YES
# If the EXTRACT_PRIVATE tag is set to YES, all private members of a class will
# be included in the documentation.
@@ -991,7 +991,7 @@ WARN_LOGFILE =
# spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
# Note: If this tag is empty the current directory is searched.
INPUT = src tests
INPUT = src tests utils/opatio
# This tag can be used to specify the character encoding of the source files
# that Doxygen parses. Internally Doxygen uses the UTF-8 encoding. Doxygen uses

16
docs/html/annotated.html
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@@ -98,16 +98,20 @@ $(document).ready(function(){initNavTree('annotated.html',''); initResizable();
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<tr id="row_2_0_1_0_" class="even"><td class="entry"><span style="width:48px;display:inline-block;">&#160;</span><span id="arr_2_0_1_0_" class="arrow" onclick="toggleFolder('2_0_1_0_')">&#9660;</span><span id="img_2_0_1_0_" class="iconfopen" onclick="toggleFolder('2_0_1_0_')">&#160;</span><a class="el" href="dir_4a32f98eb1fc28521b674ecacd8e38cc.html" target="_self">opatio</a></td><td class="desc"></td></tr>
<tr id="row_2_0_1_0_0_"><td class="entry"><span style="width:64px;display:inline-block;">&#160;</span><span id="arr_2_0_1_0_0_" class="arrow" onclick="toggleFolder('2_0_1_0_0_')">&#9660;</span><span id="img_2_0_1_0_0_" class="iconfopen" onclick="toggleFolder('2_0_1_0_0_')">&#160;</span><a class="el" href="dir_57b5236bc904b389e950b8d6ae8bc28a.html" target="_self">opat</a></td><td class="desc"></td></tr>
<tr id="row_2_0_1_0_0_0_" class="even"><td class="entry"><span style="width:96px;display:inline-block;">&#160;</span><span class="icondoc"></span><a class="el" href="src_2opatio_2opat_2____init_____8py.html" target="_self">__init__.py</a></td><td class="desc"></td></tr>
<tr id="row_2_0_1_0_0_1_"><td class="entry"><span style="width:96px;display:inline-block;">&#160;</span><span class="icondoc"></span><a class="el" href="src_2opatio_2opat_2opat_8py.html" target="_self">opat.py</a></td><td class="desc"></td></tr>
<tr id="row_2_0_1_0_1_" class="even"><td class="entry"><span style="width:80px;display:inline-block;">&#160;</span><span class="icondoc"></span><a class="el" href="src_2opatio_2____init_____8py.html" target="_self">__init__.py</a></td><td class="desc"></td></tr>
</table>
</div><!-- directory -->
</div><!-- contents -->

3
docs/html/files_dup.js
View File

@@ -1,5 +1,6 @@
var files_dup =
[
[ "src", "dir_68267d1309a1af8e8297ef4c3efbcdba.html", "dir_68267d1309a1af8e8297ef4c3efbcdba" ],
[ "tests", "dir_59425e443f801f1f2fd8bbe4959a3ccf.html", "dir_59425e443f801f1f2fd8bbe4959a3ccf" ]
[ "tests", "dir_59425e443f801f1f2fd8bbe4959a3ccf.html", "dir_59425e443f801f1f2fd8bbe4959a3ccf" ],
[ "utils", "dir_cbdb8362360e11eafe2fa3bc74cf0ffd.html", "dir_cbdb8362360e11eafe2fa3bc74cf0ffd" ]
];

191
docs/html/functions.html
View File

@@ -92,11 +92,27 @@ $(document).ready(function(){initNavTree('functions.html',''); initResizable();
</div>
<div class="contents">
<div class="textblock">Here is a list of all documented class members with links to the class documentation for each member:</div>
<div class="textblock">Here is a list of all class members with links to the classes they belong to:</div>
<h3><a id="index_b"></a>- b -</h3><ul>
<li>byteEnd
: <a class="el" href="structTableIndex.html#a69c87fd1cb0b7a64a82c52c54193e5e6">TableIndex</a>
</li>
<li>byteStart
: <a class="el" href="structTableIndex.html#ad899cf13056eb17b33e1c5e303e10132">TableIndex</a>
</li>
</ul>
<h3><a id="index_c"></a>- c -</h3><ul>
<li>constants()
: <a class="el" href="classconstants.html#a9be0748cd713f4a465b548e0c44458ee">constants</a>
<li>comment
: <a class="el" href="structHeader.html#a122331824871070af2c6cebc9698abd8">Header</a>
</li>
<li>Constant()
: <a class="el" href="structConstant.html#a84ca5b6951cc8a8eccd083894302a857">Constant</a>
</li>
<li>creationDate
: <a class="el" href="structHeader.html#a83f52dffac0449704ef1a50a5e787e92">Header</a>
</li>
</ul>
@@ -105,6 +121,12 @@ $(document).ready(function(){initNavTree('functions.html',''); initResizable();
<li>DataType
: <a class="el" href="classDObject.html#a79a2ecac4130ef3df272bdfeed26a620">DObject</a>
</li>
<li>dataTypeMap
: <a class="el" href="classDObject.html#a358d5f015da09ae5f0cbb46f3fd9e401">DObject</a>
</li>
<li>defaultObject
: <a class="el" href="classDObjectTest.html#ac753942590ae6ee456e6f3dd8b205df2">DObjectTest</a>
</li>
<li>DObject()
: <a class="el" href="classDObject.html#a0ae54853e18265657296bfb5ac3bf9d0">DObject</a>
</li>
@@ -113,12 +135,21 @@ $(document).ready(function(){initNavTree('functions.html',''); initResizable();
<h3><a id="index_g"></a>- g -</h3><ul>
<li>get()
: <a class="el" href="classconstants.html#a00666cb3d413cc53e4a3e629c2e22155">constants</a>
: <a class="el" href="classConstants.html#a36ddd7fe6857d1bbf6d1c84d4ed7bc19">Constants</a>
, <a class="el" href="classLockableDObject.html#adcfe201fc728cc1c6fcf638a566ba9a1">LockableDObject</a>
</li>
<li>getByteSize()
: <a class="el" href="classMetadata.html#ac7980d1efdd6ae434f0115f83d08348e">Metadata</a>
</li>
<li>getClosestTables()
: <a class="el" href="classOpatIO.html#a939e4edec4053517463f848648db770d">OpatIO</a>
</li>
<li>getClosestXTables()
: <a class="el" href="classOpatIO.html#a83acf4fe2aec4e588453b5a39a4def1a">OpatIO</a>
</li>
<li>getClosestZTables()
: <a class="el" href="classOpatIO.html#a9d9600e7af036deeada78da9afd4b65b">OpatIO</a>
</li>
<li>getData()
: <a class="el" href="classDObject.html#a4862655c3634d019b0a45b811d6f7235">DObject</a>
</li>
@@ -134,22 +165,43 @@ $(document).ready(function(){initNavTree('functions.html',''); initResizable();
<li>getErrorCode()
: <a class="el" href="classDObject.html#afa8926d916081de72478cb8813c25e98">DObject</a>
</li>
<li>getHeader()
: <a class="el" href="classOpatIO.html#afe725b647bc5bb802f6d711fc5dca3ab">OpatIO</a>
</li>
<li>getInstance()
: <a class="el" href="classConstants.html#aaa6f3af20fa563cf22df71a987923065">Constants</a>
</li>
<li>getMaxQDepth()
: <a class="el" href="classOpatIO.html#a48cd5e4f3fdb221bc1b6253e149e8e01">OpatIO</a>
</li>
<li>getOPATVersion()
: <a class="el" href="classOpatIO.html#a2894437c09f4cdb06c9b06d6aad4bd2f">OpatIO</a>
</li>
<li>getTable()
: <a class="el" href="classOpatIO.html#a0817f135f44e3bdc610d30df145f118d">OpatIO</a>
</li>
<li>getTableIndex()
: <a class="el" href="classOpatIO.html#af0bc6bb210c4ff74bc1e043aeb252e1a">OpatIO</a>
</li>
</ul>
<h3><a id="index_h"></a>- h -</h3><ul>
<li>has()
: <a class="el" href="classconstants.html#a35dcd5bb493bc095330b177819242c93">constants</a>
: <a class="el" href="classConstants.html#a2aa041fd223f259e55bf098c90581039">Constants</a>
</li>
<li>headerSize
: <a class="el" href="structHeader.html#af0bdf31defd5888cc8d2f7537e687917">Header</a>
</li>
</ul>
<h3><a id="index_i"></a>- i -</h3><ul>
<li>initialize()
: <a class="el" href="classconstants.html#ab08623c9c865188806b6820d3ed27fe9">constants</a>
<li>indexOffset
: <a class="el" href="structHeader.html#a31039c09176a479defcbe38597eb9957">Header</a>
</li>
<li>is_loaded()
: <a class="el" href="classconstants.html#ab72bcb21759e2e7f26f55f1d3454b999">constants</a>
<li>initializedObject
: <a class="el" href="classDObjectTest.html#a2150dd7881a4d1c68ce51344f174738e">DObjectTest</a>
</li>
<li>isDebugEnabled()
: <a class="el" href="classMetadata.html#abe52c81e04665628666b4140cd346b69">Metadata</a>
@@ -157,27 +209,55 @@ $(document).ready(function(){initNavTree('functions.html',''); initResizable();
<li>isDebuggingEnabled()
: <a class="el" href="classDObject.html#ae47bf220fbe2173cf6933c2380035dbd">DObject</a>
</li>
<li>isLoaded()
: <a class="el" href="classConstants.html#ae276dfdc0ffe75a53e3842e33ab52630">Constants</a>
, <a class="el" href="classOpatIO.html#aba1be05d51d4b0b9e4581b95ad0e1890">OpatIO</a>
</li>
</ul>
<h3><a id="index_k"></a>- k -</h3><ul>
<li>keys()
: <a class="el" href="classconstants.html#a310c5d599cf21de82eaf0abe9bc5f9a0">constants</a>
: <a class="el" href="classConstants.html#ab9de36fa145552a3e7964e7e85a67149">Constants</a>
</li>
</ul>
<h3><a id="index_l"></a>- l -</h3><ul>
<li>load()
: <a class="el" href="classOpatIO.html#a3578ac9bad40dd45ada3459f92a93b56">OpatIO</a>
</li>
<li>lock()
: <a class="el" href="classLockableDObject.html#ade38ca54703913359fc3b4366f6e292a">LockableDObject</a>
</li>
<li>LockableDObject()
: <a class="el" href="classLockableDObject.html#ae1a174a2740fa053626fe2820ee0efee">LockableDObject</a>
</li>
<li>lockableObject
: <a class="el" href="classLockableDObjectTest.html#a6f639c0023311b7900595ab11c40cd59">LockableDObjectTest</a>
</li>
<li>logKappa
: <a class="el" href="structOPATTable.html#aee4e3713cffa0ed0a5bd79e2dec97d6e">OPATTable</a>
</li>
<li>logR
: <a class="el" href="structOPATTable.html#afaf11794675d27e75de5233b947fced9">OPATTable</a>
</li>
<li>logT
: <a class="el" href="structOPATTable.html#a237ed50cee8df2144a2c47b5ffa443d3">OPATTable</a>
</li>
<li>lookupClosestTableID()
: <a class="el" href="classOpatIO.html#af870ebd76bef969fa1f7c8270ac25cd8">OpatIO</a>
</li>
<li>lookupTableID()
: <a class="el" href="classOpatIO.html#a37959ed6845e09302bb8c206e3e006e4">OpatIO</a>
</li>
</ul>
<h3><a id="index_m"></a>- m -</h3><ul>
<li>magic
: <a class="el" href="structHeader.html#a87c9fc5b27c41fe65698f8538c23b182">Header</a>
</li>
<li>Metadata()
: <a class="el" href="classMetadata.html#ae849560667461008cb72e83919c20be0">Metadata</a>
</li>
@@ -185,19 +265,32 @@ $(document).ready(function(){initNavTree('functions.html',''); initResizable();
<h3><a id="index_n"></a>- n -</h3><ul>
<li>N_R
: <a class="el" href="structOPATTable.html#a70b70699726b2f77b486702e913a164b">OPATTable</a>
</li>
<li>N_T
: <a class="el" href="structOPATTable.html#a87cc2d8e225e5e9c567602d779aec88f">OPATTable</a>
</li>
<li>name
: <a class="el" href="structconstant.html#af52cfa5a80b3641881d45eef6d597510">constant</a>
: <a class="el" href="structConstant.html#a8d8d2a81e9a8f36dfa02b4d23a5be55c">Constant</a>
</li>
<li>numTables
: <a class="el" href="structHeader.html#a162ced3913c3373d6d54c32274b99d72">Header</a>
</li>
</ul>
<h3><a id="index_o"></a>- o -</h3><ul>
<li>OpatIO()
: <a class="el" href="classOpatIO.html#a7f3436b3ac0dbe141b08d8064550f1b3">OpatIO</a>
</li>
<li>operator&lt;&lt;
: <a class="el" href="classDObject.html#a5b2896a287295bf59a0b9e4d0af21161">DObject</a>
: <a class="el" href="structConstant.html#ad298f7af7cdfd2e2267fd9e464558e2b">Constant</a>
, <a class="el" href="classDObject.html#a5b2896a287295bf59a0b9e4d0af21161">DObject</a>
, <a class="el" href="classMetadata.html#a9bc49cc23da2d1ff8b3e197630b9dfd2">Metadata</a>
</li>
<li>operator[]()
: <a class="el" href="classconstants.html#a32d515b1f539f6fdfc654ed5c8cba8e0">constants</a>
: <a class="el" href="classConstants.html#ad75620743b867fc20d4a05027d1a1c01">Constants</a>
</li>
</ul>
@@ -206,16 +299,28 @@ $(document).ready(function(){initNavTree('functions.html',''); initResizable();
<li>Plugin
: <a class="el" href="classDObject.html#af11334d08ef85c68b3aae7554548e5a7">DObject</a>
</li>
<li>printHeader()
: <a class="el" href="classOpatIO.html#a117f7e1f45d6c410c21d0644e447bbb1">OpatIO</a>
</li>
<li>printTable()
: <a class="el" href="classOpatIO.html#aa8037fc93588dd4c6cbec9bb7c76225f">OpatIO</a>
</li>
<li>printTableIndex()
: <a class="el" href="classOpatIO.html#afa623ba10f188097e555a682a4c69a9f">OpatIO</a>
</li>
</ul>
<h3><a id="index_r"></a>- r -</h3><ul>
<li>reference
: <a class="el" href="structconstant.html#a6be3abe8a0b5a3057d1ab572bd7aad76">constant</a>
: <a class="el" href="structConstant.html#a1c7e6c5a1d2316c98e59e04a234754d1">Constant</a>
</li>
<li>registerPlugin()
: <a class="el" href="classDObject.html#a15afffdf339150fc872bf63bdd08d581">DObject</a>
</li>
<li>reserved
: <a class="el" href="structHeader.html#af99697d38997984f2295c902d3ce1772">Header</a>
</li>
<li>runAllPlugins()
: <a class="el" href="classDObject.html#a1223275dcbbf20334ea11707346acb93">DObject</a>
</li>
@@ -247,15 +352,43 @@ $(document).ready(function(){initNavTree('functions.html',''); initResizable();
<li>setErrorCode()
: <a class="el" href="classDObject.html#a3dce47a519f9da5085c0c5ac1eea4f38">DObject</a>
</li>
<li>setFilename()
: <a class="el" href="classOpatIO.html#ad189e0f239bc4184fecf7daef7923272">OpatIO</a>
</li>
<li>setMaxQDepth()
: <a class="el" href="classOpatIO.html#ab0edd41690b8d5c1775f87439cf82cb5">OpatIO</a>
</li>
<li>SetUp()
: <a class="el" href="classconstTest.html#af4753885bf401953202f89d455a2702f">constTest</a>
, <a class="el" href="classDObjectTest.html#a95ba0f78c44e0bd46603de32028b7be6">DObjectTest</a>
, <a class="el" href="classLockableDObjectTest.html#a4ca643fb176141b51f4761dd3df64769">LockableDObjectTest</a>
, <a class="el" href="classMetadataTest.html#a6273a370a10b42155af951a8fc2c47fa">MetadataTest</a>
</li>
<li>sha256
: <a class="el" href="structTableIndex.html#a0c4826e48839977fa2bfaa1bf51b6cdb">TableIndex</a>
</li>
<li>sourceInfo
: <a class="el" href="structHeader.html#ac1a0c67ed5bd4021581fc00c2d79dba3">Header</a>
</li>
</ul>
<h3><a id="index_t"></a>- t -</h3><ul>
<li>TearDown()
: <a class="el" href="classMetadataTest.html#a24075d61d37dceacd353ecde16a1ac71">MetadataTest</a>
</li>
</ul>
<h3><a id="index_u"></a>- u -</h3><ul>
<li>uncertainty
: <a class="el" href="structconstant.html#aa23b68117657bec4bb8409eb30d1b3e4">constant</a>
: <a class="el" href="structConstant.html#a0ae09f22af150a41aa4169a4a60933be">Constant</a>
</li>
<li>unit
: <a class="el" href="structconstant.html#ace4a7f2bfc5b80a76c494e92349f9048">constant</a>
: <a class="el" href="structConstant.html#a2c46956a2d2b0ebf78ff99c5971130d2">Constant</a>
</li>
<li>unload()
: <a class="el" href="classOpatIO.html#ac1c1a6159f82462fedf9b526ddcc19a6">OpatIO</a>
</li>
<li>unlock()
: <a class="el" href="classLockableDObject.html#a1481ed99dcd837490bf28309aadaedfb">LockableDObject</a>
@@ -268,7 +401,31 @@ $(document).ready(function(){initNavTree('functions.html',''); initResizable();
<h3><a id="index_v"></a>- v -</h3><ul>
<li>value
: <a class="el" href="structconstant.html#a81804eeeca08f157af92766d5285064f">constant</a>
: <a class="el" href="structConstant.html#a3bda8d7fadd6fb2510fd39962a065a02">Constant</a>
</li>
<li>version
: <a class="el" href="structHeader.html#ac55e763f9e96050f4dab115a4a1c2356">Header</a>
</li>
</ul>
<h3><a id="index_x"></a>- x -</h3><ul>
<li>X
: <a class="el" href="structTableIndex.html#a303592792b2490da4105e294fb4666ca">TableIndex</a>
</li>
</ul>
<h3><a id="index_z"></a>- z -</h3><ul>
<li>Z
: <a class="el" href="structTableIndex.html#a7271de867fee8bb48a71f70afebbf0bd">TableIndex</a>
</li>
</ul>
<h3><a id="index__7E"></a>- ~ -</h3><ul>
<li>~OpatIO()
: <a class="el" href="classOpatIO.html#ac34f611a9eab458329553d27e8bffec6">OpatIO</a>
</li>
</ul>
</div><!-- contents -->

103
docs/html/functions_func.html
View File

@@ -95,8 +95,8 @@ $(document).ready(function(){initNavTree('functions_func.html',''); initResizabl
&#160;
<h3><a id="index_c"></a>- c -</h3><ul>
<li>constants()
: <a class="el" href="classconstants.html#a9be0748cd713f4a465b548e0c44458ee">constants</a>
<li>Constant()
: <a class="el" href="structConstant.html#a84ca5b6951cc8a8eccd083894302a857">Constant</a>
</li>
</ul>
@@ -110,12 +110,21 @@ $(document).ready(function(){initNavTree('functions_func.html',''); initResizabl
<h3><a id="index_g"></a>- g -</h3><ul>
<li>get()
: <a class="el" href="classconstants.html#a00666cb3d413cc53e4a3e629c2e22155">constants</a>
: <a class="el" href="classConstants.html#a36ddd7fe6857d1bbf6d1c84d4ed7bc19">Constants</a>
, <a class="el" href="classLockableDObject.html#adcfe201fc728cc1c6fcf638a566ba9a1">LockableDObject</a>
</li>
<li>getByteSize()
: <a class="el" href="classMetadata.html#ac7980d1efdd6ae434f0115f83d08348e">Metadata</a>
</li>
<li>getClosestTables()
: <a class="el" href="classOpatIO.html#a939e4edec4053517463f848648db770d">OpatIO</a>
</li>
<li>getClosestXTables()
: <a class="el" href="classOpatIO.html#a83acf4fe2aec4e588453b5a39a4def1a">OpatIO</a>
</li>
<li>getClosestZTables()
: <a class="el" href="classOpatIO.html#a9d9600e7af036deeada78da9afd4b65b">OpatIO</a>
</li>
<li>getData()
: <a class="el" href="classDObject.html#a4862655c3634d019b0a45b811d6f7235">DObject</a>
</li>
@@ -131,46 +140,71 @@ $(document).ready(function(){initNavTree('functions_func.html',''); initResizabl
<li>getErrorCode()
: <a class="el" href="classDObject.html#afa8926d916081de72478cb8813c25e98">DObject</a>
</li>
<li>getHeader()
: <a class="el" href="classOpatIO.html#afe725b647bc5bb802f6d711fc5dca3ab">OpatIO</a>
</li>
<li>getInstance()
: <a class="el" href="classConstants.html#aaa6f3af20fa563cf22df71a987923065">Constants</a>
</li>
<li>getMaxQDepth()
: <a class="el" href="classOpatIO.html#a48cd5e4f3fdb221bc1b6253e149e8e01">OpatIO</a>
</li>
<li>getOPATVersion()
: <a class="el" href="classOpatIO.html#a2894437c09f4cdb06c9b06d6aad4bd2f">OpatIO</a>
</li>
<li>getTable()
: <a class="el" href="classOpatIO.html#a0817f135f44e3bdc610d30df145f118d">OpatIO</a>
</li>
<li>getTableIndex()
: <a class="el" href="classOpatIO.html#af0bc6bb210c4ff74bc1e043aeb252e1a">OpatIO</a>
</li>
</ul>
<h3><a id="index_h"></a>- h -</h3><ul>
<li>has()
: <a class="el" href="classconstants.html#a35dcd5bb493bc095330b177819242c93">constants</a>
: <a class="el" href="classConstants.html#a2aa041fd223f259e55bf098c90581039">Constants</a>
</li>
</ul>
<h3><a id="index_i"></a>- i -</h3><ul>
<li>initialize()
: <a class="el" href="classconstants.html#ab08623c9c865188806b6820d3ed27fe9">constants</a>
</li>
<li>is_loaded()
: <a class="el" href="classconstants.html#ab72bcb21759e2e7f26f55f1d3454b999">constants</a>
</li>
<li>isDebugEnabled()
: <a class="el" href="classMetadata.html#abe52c81e04665628666b4140cd346b69">Metadata</a>
</li>
<li>isDebuggingEnabled()
: <a class="el" href="classDObject.html#ae47bf220fbe2173cf6933c2380035dbd">DObject</a>
</li>
<li>isLoaded()
: <a class="el" href="classConstants.html#ae276dfdc0ffe75a53e3842e33ab52630">Constants</a>
, <a class="el" href="classOpatIO.html#aba1be05d51d4b0b9e4581b95ad0e1890">OpatIO</a>
</li>
</ul>
<h3><a id="index_k"></a>- k -</h3><ul>
<li>keys()
: <a class="el" href="classconstants.html#a310c5d599cf21de82eaf0abe9bc5f9a0">constants</a>
: <a class="el" href="classConstants.html#ab9de36fa145552a3e7964e7e85a67149">Constants</a>
</li>
</ul>
<h3><a id="index_l"></a>- l -</h3><ul>
<li>load()
: <a class="el" href="classOpatIO.html#a3578ac9bad40dd45ada3459f92a93b56">OpatIO</a>
</li>
<li>lock()
: <a class="el" href="classLockableDObject.html#ade38ca54703913359fc3b4366f6e292a">LockableDObject</a>
</li>
<li>LockableDObject()
: <a class="el" href="classLockableDObject.html#ae1a174a2740fa053626fe2820ee0efee">LockableDObject</a>
</li>
<li>lookupClosestTableID()
: <a class="el" href="classOpatIO.html#af870ebd76bef969fa1f7c8270ac25cd8">OpatIO</a>
</li>
<li>lookupTableID()
: <a class="el" href="classOpatIO.html#a37959ed6845e09302bb8c206e3e006e4">OpatIO</a>
</li>
</ul>
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<h3><a id="index_o"></a>- o -</h3><ul>
<li>OpatIO()
: <a class="el" href="classOpatIO.html#a7f3436b3ac0dbe141b08d8064550f1b3">OpatIO</a>
</li>
<li>operator[]()
: <a class="el" href="classconstants.html#a32d515b1f539f6fdfc654ed5c8cba8e0">constants</a>
: <a class="el" href="classConstants.html#ad75620743b867fc20d4a05027d1a1c01">Constants</a>
</li>
</ul>
<h3><a id="index_p"></a>- p -</h3><ul>
<li>printHeader()
: <a class="el" href="classOpatIO.html#a117f7e1f45d6c410c21d0644e447bbb1">OpatIO</a>
</li>
<li>printTable()
: <a class="el" href="classOpatIO.html#aa8037fc93588dd4c6cbec9bb7c76225f">OpatIO</a>
</li>
<li>printTableIndex()
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</li>
</ul>
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</li>
<li>setFilename()
: <a class="el" href="classOpatIO.html#ad189e0f239bc4184fecf7daef7923272">OpatIO</a>
</li>
<li>setMaxQDepth()
: <a class="el" href="classOpatIO.html#ab0edd41690b8d5c1775f87439cf82cb5">OpatIO</a>
</li>
<li>SetUp()
: <a class="el" href="classconstTest.html#af4753885bf401953202f89d455a2702f">constTest</a>
, <a class="el" href="classDObjectTest.html#a95ba0f78c44e0bd46603de32028b7be6">DObjectTest</a>
, <a class="el" href="classLockableDObjectTest.html#a4ca643fb176141b51f4761dd3df64769">LockableDObjectTest</a>
, <a class="el" href="classMetadataTest.html#a6273a370a10b42155af951a8fc2c47fa">MetadataTest</a>
</li>
</ul>
<h3><a id="index_t"></a>- t -</h3><ul>
<li>TearDown()
: <a class="el" href="classMetadataTest.html#a24075d61d37dceacd353ecde16a1ac71">MetadataTest</a>
</li>
</ul>
<h3><a id="index_u"></a>- u -</h3><ul>
<li>unload()
: <a class="el" href="classOpatIO.html#ac1c1a6159f82462fedf9b526ddcc19a6">OpatIO</a>
</li>
<li>unlock()
: <a class="el" href="classLockableDObject.html#a1481ed99dcd837490bf28309aadaedfb">LockableDObject</a>
</li>
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: <a class="el" href="classDObject.html#a99b8688849e11501033a25f61efb8356">DObject</a>
</li>
</ul>
<h3><a id="index__7E"></a>- ~ -</h3><ul>
<li>~OpatIO()
: <a class="el" href="classOpatIO.html#ac34f611a9eab458329553d27e8bffec6">OpatIO</a>
</li>
</ul>
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</div><!-- doc-content -->
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3
docs/html/functions_rela.html
View File

@@ -94,7 +94,8 @@ $(document).ready(function(){initNavTree('functions_rela.html',''); initResizabl
<div class="contents">
&#160;<ul>
<li>operator&lt;&lt;
: <a class="el" href="classDObject.html#a5b2896a287295bf59a0b9e4d0af21161">DObject</a>
: <a class="el" href="structConstant.html#ad298f7af7cdfd2e2267fd9e464558e2b">Constant</a>
, <a class="el" href="classDObject.html#a5b2896a287295bf59a0b9e4d0af21161">DObject</a>
, <a class="el" href="classMetadata.html#a9bc49cc23da2d1ff8b3e197630b9dfd2">Metadata</a>
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60
docs/html/globals.html
View File

@@ -92,19 +92,65 @@ $(document).ready(function(){initNavTree('globals.html',''); initResizable(); })
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<div class="contents">
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<div class="textblock">Here is a list of all file members with links to the files they belong to:</div>
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</li>
<li>is_big_endian()
: <a class="el" href="opatIO_8cpp.html#aed5f3e73e01248d8a2d6792a69081f9e">opatIO.cpp</a>
</li>
</ul>
<h3><a id="index_m"></a>- m -</h3><ul>
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</li>
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<h3><a id="index_o"></a>- o -</h3><ul>
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</li>
<li>operator&lt;&lt;()
: <a class="el" href="DObject_8cpp.html#a5b2896a287295bf59a0b9e4d0af21161">DObject.cpp</a>
, <a class="el" href="Metadata_8cpp.html#a9bc49cc23da2d1ff8b3e197630b9dfd2">Metadata.cpp</a>
</li>
</ul>
<h3><a id="index_s"></a>- s -</h3><ul>
<li>swap_bytes()
: <a class="el" href="opatIO_8cpp.html#a33dcb837958721219b4198c267c7fd0f">opatIO.cpp</a>
</li>
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<h3><a id="index_t"></a>- t -</h3><ul>
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, <a class="el" href="MetadataTest_8cpp.html#a8854bc3bdde52a7c73927f17e4330a89">MetadataTest.cpp</a>
, <a class="el" href="LockableDObjectTest_8cpp.html#a5c2342bfafc553d23125fb3ae05af2a7">LockableDObjectTest.cpp</a>
: <a class="el" href="MetadataTest_8cpp.html#a8854bc3bdde52a7c73927f17e4330a89">MetadataTest.cpp</a>
, <a class="el" href="constTest_8cpp.html#a92b56f4876b91eb7d628492fe220babb">constTest.cpp</a>
, <a class="el" href="opatIOTest_8cpp.html#ac3a79e8bac7362518c4495f4b9136a99">opatIOTest.cpp</a>
, <a class="el" href="LockableDObjectTest_8cpp.html#a8b547408c52b669c3c220aa640927474">LockableDObjectTest.cpp</a>
, <a class="el" href="constTest_8cpp.html#ae050a185fbc60349459af47e661bd3e1">constTest.cpp</a>
, <a class="el" href="LockableDObjectTest_8cpp.html#a470f4e60873d3ea6afc7c319e307760f">LockableDObjectTest.cpp</a>
, <a class="el" href="DObjectTest_8cpp.html#ab0d7e76fe973dea21f97cf26d3b3847b">DObjectTest.cpp</a>
, <a class="el" href="constTest_8cpp.html#a6855bb766d336a17d11e54111ebcb225">constTest.cpp</a>
, <a class="el" href="DObjectTest_8cpp.html#a3fc628b3943158a063739c03a4c2ca1f">DObjectTest.cpp</a>
, <a class="el" href="LockableDObjectTest_8cpp.html#a5c694ab0fb07081c02cac1f0bc3f3e73">LockableDObjectTest.cpp</a>
</li>
<li>testFunction()
: <a class="el" href="testDObject_8cpp.html#a5cce1ff8e67a00ce9122097c4bbb5b02">testDObject.cpp</a>
</li>
</ul>
</div><!-- contents -->

47
docs/html/globals_func.html
View File

@@ -92,19 +92,52 @@ $(document).ready(function(){initNavTree('globals_func.html',''); initResizable(
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&#160;<ul>
&#160;
<h3><a id="index_i"></a>- i -</h3><ul>
<li>initlaize_opac()
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</li>
<li>is_big_endian()
: <a class="el" href="opatIO_8cpp.html#aed5f3e73e01248d8a2d6792a69081f9e">opatIO.cpp</a>
</li>
</ul>
<h3><a id="index_m"></a>- m -</h3><ul>
<li>main()
: <a class="el" href="testDObject_8cpp.html#ae66f6b31b5ad750f1fe042a706a4e3d4">testDObject.cpp</a>
</li>
</ul>
<h3><a id="index_o"></a>- o -</h3><ul>
<li>operator&lt;&lt;()
: <a class="el" href="DObject_8cpp.html#a5b2896a287295bf59a0b9e4d0af21161">DObject.cpp</a>
, <a class="el" href="Metadata_8cpp.html#a9bc49cc23da2d1ff8b3e197630b9dfd2">Metadata.cpp</a>
</li>
</ul>
<h3><a id="index_s"></a>- s -</h3><ul>
<li>swap_bytes()
: <a class="el" href="opatIO_8cpp.html#a33dcb837958721219b4198c267c7fd0f">opatIO.cpp</a>
</li>
</ul>
<h3><a id="index_t"></a>- t -</h3><ul>
<li>TEST_F()
: <a class="el" href="LockableDObjectTest_8cpp.html#aca2c2dcb4394094c27dc37453ea9a37f">LockableDObjectTest.cpp</a>
, <a class="el" href="MetadataTest_8cpp.html#a8854bc3bdde52a7c73927f17e4330a89">MetadataTest.cpp</a>
, <a class="el" href="LockableDObjectTest_8cpp.html#a5c2342bfafc553d23125fb3ae05af2a7">LockableDObjectTest.cpp</a>
: <a class="el" href="MetadataTest_8cpp.html#a8854bc3bdde52a7c73927f17e4330a89">MetadataTest.cpp</a>
, <a class="el" href="constTest_8cpp.html#a92b56f4876b91eb7d628492fe220babb">constTest.cpp</a>
, <a class="el" href="opatIOTest_8cpp.html#ac3a79e8bac7362518c4495f4b9136a99">opatIOTest.cpp</a>
, <a class="el" href="LockableDObjectTest_8cpp.html#a8b547408c52b669c3c220aa640927474">LockableDObjectTest.cpp</a>
, <a class="el" href="constTest_8cpp.html#ae050a185fbc60349459af47e661bd3e1">constTest.cpp</a>
, <a class="el" href="LockableDObjectTest_8cpp.html#a470f4e60873d3ea6afc7c319e307760f">LockableDObjectTest.cpp</a>
, <a class="el" href="DObjectTest_8cpp.html#ab0d7e76fe973dea21f97cf26d3b3847b">DObjectTest.cpp</a>
, <a class="el" href="constTest_8cpp.html#a6855bb766d336a17d11e54111ebcb225">constTest.cpp</a>
, <a class="el" href="DObjectTest_8cpp.html#a3fc628b3943158a063739c03a4c2ca1f">DObjectTest.cpp</a>
, <a class="el" href="LockableDObjectTest_8cpp.html#a5c694ab0fb07081c02cac1f0bc3f3e73">LockableDObjectTest.cpp</a>
</li>
<li>testFunction()
: <a class="el" href="testDObject_8cpp.html#a5cce1ff8e67a00ce9122097c4bbb5b02">testDObject.cpp</a>
</li>
</ul>
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9
docs/html/navtreedata.js
View File

@@ -25,6 +25,11 @@
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\doxysection{Class List}
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\item\contentsline{section}{\mbox{\hyperlink{classCell}{Cell}} }{\pageref{classCell}}{}
\item\contentsline{section}{\mbox{\hyperlink{structconstant}{constant}} \\*Structure to hold a constant\textquotesingle{}s details }{\pageref{structconstant}}{}
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\item\contentsline{section}{\mbox{\hyperlink{classLockableDObject}{Lockable\+DObject}} \\*Wrapper for \mbox{\hyperlink{classDObject}{DObject}} with thread-\/safe access }{\pageref{classLockableDObject}}{}
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\doxysection{File List}
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\item\contentsline{section}{src/const/public/{\bfseries const.\+h} }{\pageref{const_8h}}{}
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\item\contentsline{section}{src/mapping/private/{\bfseries grid.\+h} }{\pageref{grid_8h}}{}
\item\contentsline{section}{src/mapping/private/{\bfseries mapper.\+h} }{\pageref{mapper_8h}}{}
\item\contentsline{section}{src/mesh/public/{\bfseries mesh.\+h} }{\pageref{mesh_8h}}{}
\item\contentsline{section}{src/opac/public/{\bfseries opac.\+h} }{\pageref{opac_8h}}{}
\item\contentsline{section}{src/opac/public/\mbox{\hyperlink{opac_8h}{opac.\+h}} }{\pageref{opac_8h}}{}
\item\contentsline{section}{src/opat\+IO/private/\mbox{\hyperlink{opatIO_8cpp}{opat\+IO.\+cpp}} }{\pageref{opatIO_8cpp}}{}
\item\contentsline{section}{src/opat\+IO/public/\mbox{\hyperlink{opatIO_8h}{opat\+IO.\+h}} }{\pageref{opatIO_8h}}{}
\item\contentsline{section}{tests/const/\mbox{\hyperlink{constTest_8cpp}{const\+Test.\+cpp}} \\*Unit tests for the const class }{\pageref{constTest_8cpp}}{}
\item\contentsline{section}{tests/dobj/\mbox{\hyperlink{DObjectTest_8cpp}{DObject\+Test.\+cpp}} \\*Unit tests for the \mbox{\hyperlink{classDObject}{DObject}} class }{\pageref{DObjectTest_8cpp}}{}
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\item\contentsline{section}{utils/opatio/build/lib/opatio/opat/\mbox{\hyperlink{build_2lib_2opatio_2opat_2____init_____8py}{\+\_\+\+\_\+init\+\_\+\+\_\+.\+py}} }{\pageref{build_2lib_2opatio_2opat_2____init_____8py}}{}
\item\contentsline{section}{utils/opatio/build/lib/opatio/opat/\mbox{\hyperlink{build_2lib_2opatio_2opat_2opat_8py}{opat.\+py}} }{\pageref{build_2lib_2opatio_2opat_2opat_8py}}{}
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%--- Begin generated contents ---
\chapter{opat\+IO python module}
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\input{classDObjectTest}
\input{structHeader}
\input{classLockableDObject}
\input{classLockableDObjectTest}
\input{classMetadata}
\input{classMetadataTest}
\input{classOpatIO}
\input{classopatIOTest}
\input{structOPATTable}
\input{structTableIndex}
\chapter{File Documentation}
\input{const_8cpp}
\input{const_8h}
\input{DObject_8cpp}
\input{LockableDObject_8cpp}
\input{Metadata_8cpp}
\input{DObject_8h}
\input{LockableDObject_8h}
\input{Metadata_8h}
\input{opac_8h}
\input{opatIO_8cpp}
\input{opatIO_8h}
\input{constTest_8cpp}
\input{DObjectTest_8cpp}
\input{LockableDObjectTest_8cpp}
\input{MetadataTest_8cpp}
\input{testDObject_8cpp}
\input{opatIOTest_8cpp}
\input{build_2lib_2opatio_2____init_____8py}
\input{build_2lib_2opatio_2opat_2____init_____8py}
\input{src_2opatio_2____init_____8py}
\input{src_2opatio_2opat_2____init_____8py}
\input{build_2lib_2opatio_2opat_2opat_8py}
\input{src_2opatio_2opat_2opat_8py}
\input{readme_8md}
%--- End generated contents ---
% Index

237
src/opatIO/public/opatIO.h
View File

@@ -9,93 +9,264 @@
#include <map>
#include <utility>
/**
* @brief Structure to hold the header information of an OPAT file.
*/
#pragma pack(1)
struct Header {
char magic[4];
uint16_t version;
uint32_t numTables;
uint32_t headerSize;
uint64_t indexOffset;
char creationDate[16];
char sourceInfo[64];
char comment[128];
char reserved[26];
char magic[4]; ///< Magic number to identify the file type
uint16_t version; ///< Version of the OPAT file format
uint32_t numTables; ///< Number of tables in the file
uint32_t headerSize; ///< Size of the header
uint64_t indexOffset; ///< Offset to the index section
char creationDate[16]; ///< Creation date of the file
char sourceInfo[64]; ///< Source information
char comment[128]; ///< Comment section
char reserved[26]; ///< Reserved for future use
};
#pragma pack()
/**
* @brief Structure to hold the index information of a table in an OPAT file.
*/
struct TableIndex {
double X;
double Z;
// double C; // For type 2 OPAL tables. When not set will be 0
// double O; // For type 2 OPAL tables. When not set will be 0
uint64_t byteStart;
uint64_t byteEnd;
char sha256[32];
double X; ///< X composition value
double Z; ///< Z composition value
uint64_t byteStart; ///< Byte start position of the table
uint64_t byteEnd; ///< Byte end position of the table
char sha256[32]; ///< SHA-256 hash of the table data
};
/**
* @brief Structure to hold the data of an OPAT table.
*/
struct OPATTable {
uint32_t N_R;
uint32_t N_T;
std::vector<double> logR;
std::vector<double> logT;
std::vector<std::vector<double>> logKappa;
uint32_t N_R; ///< Number of R values
uint32_t N_T; ///< Number of T values
std::vector<double> logR; ///< Logarithm of R values
std::vector<double> logT; ///< Logarithm of T values
std::vector<std::vector<double>> logKappa; ///< Logarithm of Kappa values
};
class opatIOTest; // Friend for gtest
/**
* @brief Class to manage the input/output operations for OPAT files.
*/
class OpatIO {
private:
Header header;
std::vector<TableIndex> tableIndex;
std::deque<std::pair<int, OPATTable>> tableQueue;
std::map<int, std::pair<double, double>> tableIDToComposition;
std::pair<double, double> XZepsilon;
int maxQDepth = 10;
std::string filename;
bool loaded = false;
Header header; ///< Header information of the OPAT file
std::vector<TableIndex> tableIndex; ///< Index information of the tables
std::deque<std::pair<int, OPATTable>> tableQueue; ///< Queue to manage table caching
std::map<int, std::pair<double, double>> tableIDToComposition; ///< Map to store table ID to composition mapping
std::pair<double, double> XZepsilon; ///< Epsilon values for X and Z
int maxQDepth = 10; ///< Maximum depth of the table queue
std::string filename; ///< Filename of the OPAT file
bool loaded = false; ///< Flag to indicate if the file is loaded
/**
* @brief Read the header from the file.
* @param file The input file stream.
*/
void readHeader(std::ifstream &file);
/**
* @brief Read the table index from the file.
* @param file The input file stream.
*/
void readTableIndex(std::ifstream &file);
/**
* @brief Get a table from the queue.
* @param tableID The ID of the table.
* @return The OPAT table.
*/
OPATTable getTableFromQueue(int tableID);
/**
* @brief Add a table to the queue.
* @param tableID The ID of the table.
* @param table The OPAT table.
*/
void addTableToQueue(int tableID, OPATTable table);
/**
* @brief Remove a table from the queue.
*/
void removeTableFromQueue();
/**
* @brief Flush the table queue.
*/
void flushQueue();
/**
* @brief Get a table by its ID.
* @param tableID The ID of the table.
* @return The OPAT table.
*/
OPATTable getTable(int tableID);
/**
* @brief Print a table.
* @param table The OPAT table.
* @param truncateDigits Number of digits to truncate.
*/
void printTable(OPATTable table, uint32_t truncateDigits=5);
/**
* @brief Lookup epsilon values for X and Z.
*/
void XZLookupEpsilon();
/**
* @brief Build the table ID to composition mapping.
*/
void buildTableIDToComposition();
public:
/**
* @brief Default constructor.
*/
OpatIO();
/**
* @brief Constructor with filename.
* @param filename The name of the OPAT file.
*/
OpatIO(std::string filename);
/**
* @brief Destructor.
*/
~OpatIO();
/**
* @brief Get a table by X and Z values.
* @param X The X composition value.
* @param Z The Z composition value.
* @return The OPAT table.
*/
OPATTable getTable(double X, double Z);
/**
* @brief Set the maximum depth of the table queue.
* @param depth The maximum depth.
*/
void setMaxQDepth(int depth);
/**
* @brief Get the maximum depth of the table queue.
* @return The maximum depth.
*/
int getMaxQDepth();
/**
* @brief Set the filename of the OPAT file.
* @param filename The name of the file.
*/
void setFilename(std::string filename);
/**
* @brief Load the OPAT file.
*/
void load();
/**
* @brief Unload the OPAT file.
*/
void unload();
/**
* @brief Check if the file is loaded.
* @return True if the file is loaded, false otherwise.
*/
bool isLoaded();
/**
* @brief Print the header information.
*/
void printHeader();
/**
* @brief Print the table index.
*/
void printTableIndex();
/**
* @brief Print a table by X and Z values.
* @param X The X composition value.
* @param Z The Z composition value.
* @param truncateDigits Number of digits to truncate.
*/
void printTable(double X, double Z, uint32_t truncateDigits=5);
/**
* @brief Get the table index.
* @return A vector of TableIndex structures.
*/
std::vector<TableIndex> getTableIndex();
/**
* @brief Get the header information.
* @return The Header structure.
*/
Header getHeader();
/**
* @brief Get the closest tables by X value.
* @param X The X composition value.
* @param ZExact The exact Z composition value.
* @param C The C composition value (default is 0).
* @param O The O composition value (default is 0).
* @param numTables The number of closest tables to retrieve (default is 1).
* @return A vector of OPAT tables.
*/
std::vector<OPATTable> getClosestXTables(double X, double ZExact, double C=0, double O=0, int numTables=1);
std::vector<OPATTable> getClosestZTables(double XExact, double Z, double C=0, double O=0, int numTables=1);
std::vector<OPATTable> getClosestTables(double X, double Z, double C=0, double O=0, int numTables=1);
/**
* @brief Get the closest tables by Z value.
* @param XExact The exact X composition value.
* @param Z The Z composition value.
* @param C The C composition value (default is 0).
* @param O The O composition value (default is 0).
* @param numTables The number of closest tables to retrieve (default is 1).
* @return A vector of OPAT tables.
*/
std::vector<OPATTable> getClosestZTables(double XExact, double Z, double C=0, double O=0, int numTables=1);
/**
* @brief Get the closest tables by X and Z values.
* @param X The X composition value.
* @param Z The Z composition value.
* @param C The C composition value (default is 0).
* @param O The O composition value (default is 0).
* @param numTables The number of closest tables to retrieve (default is 1).
* @return A vector of OPAT tables.
*/
std::vector<OPATTable> getClosestTables(double X, double Z, double C=0, double O=0, int numTables=1);
/**
* @brief Lookup the table ID by X and Z values.
* @param X The X composition value.
* @param Z The Z composition value.
* @return The table ID.
*/
int lookupTableID(double X, double Z);
/**
* @brief Lookup the closest table ID by X and Z values.
* @param X The X composition value.
* @param Z The Z composition value.
* @return The closest table ID.
*/
int lookupClosestTableID(double X, double Z);
/**
* @brief Get the version of the OPAT file format.
* @return The version of the OPAT file format.
*/
uint16_t getOPATVersion();
};
#endif

156
utils/opatio/src/opatio/opat/opat.py
View File

@@ -13,31 +13,40 @@ import os
@dataclass
class Header:
magic: str
version: int
numTables: int
headerSize: int
indexOffset: int
creationDate: str
sourceInfo: str
comment: str
reserved: bytes
"""
@brief Structure to hold the header information of an OPAT file.
"""
magic: str #< Magic number to identify the file type
version: int #< Version of the OPAT file format
numTables: int #< Number of tables in the file
headerSize: int #< Size of the header
indexOffset: int #< Offset to the index section
creationDate: str #< Creation date of the file
sourceInfo: str #< Source information
comment: str #< Comment section
reserved: bytes #< Reserved for future use
@dataclass
class TableIndex:
X: float
Z: float
byteStart: int
byteEnd: int
sha256: bytes
"""
@brief Structure to hold the index information of a table in an OPAT file.
"""
X: float #< X composition value
Z: float #< Z composition value
byteStart: int #< Byte start position of the table
byteEnd: int #< Byte end position of the table
sha256: bytes #< SHA-256 hash of the table data
@dataclass
class OPATTable:
N_R: int
N_T: int
logR: Iterable[float]
logT: Iterable[float]
logKappa: Iterable[Iterable[float]]
"""
@brief Structure to hold the data of an OPAT table.
"""
N_R: int #< Number of R values
N_T: int #< Number of T values
logR: Iterable[float] #< Logarithm of R values
logT: Iterable[float] #< Logarithm of T values
logKappa: Iterable[Iterable[float]] #< Logarithm of Kappa values
defaultHeader = Header(
magic="OPAT",
@@ -58,19 +67,31 @@ class OpatIO:
@staticmethod
def validate_char_array_size(s: str, nmax: int) -> bool:
"""
@brief Validate the size of a character array.
@param s The string to validate.
@param nmax The maximum allowed size.
@return True if the string size is valid, False otherwise.
"""
if len(s) > nmax:
return False
return True
@staticmethod
def validate_logKappa(logKappa):
"""
@brief Validate the logKappa array.
@param logKappa The logKappa array to validate.
@throws ValueError if logKappa is not a non-empty 2D array.
@throws TypeError if logKappa is not a 2D array or iterable.
"""
if isinstance(logKappa, np.ndarray):
if logKappa.ndim == 2:
return
else:
raise ValueError("logKappa must be a non-empty 2D array")
if isintance(logKappa, collectionIterable) and all(isinstance(row, collectionIterable) for row in logKappa):
if isinstance(logKappa, collectionIterable) and all(isinstance(row, collectionIterable) for row in logKappa):
try:
first_row = next(iter(logKappa))
if all(isinstance(x, (int, float)) for x in first_row):
@@ -84,6 +105,13 @@ class OpatIO:
@staticmethod
def validate_1D(arr, name: str):
"""
@brief Validate a 1D array.
@param arr The array to validate.
@param name The name of the array.
@throws ValueError if the array is not 1D or not fully numeric.
@throws TypeError if the array is not a non-empty 1D array or iterable.
"""
if isinstance(arr, np.ndarray):
if arr.ndim == 1:
return
@@ -95,29 +123,60 @@ class OpatIO:
else:
raise ValueError(f"{name} must be fully numeric")
else:
raise TypeError(f"{name} must be a non-empty 2D array or iterable")
raise TypeError(f"{name} must be a non-empty 1D array or iterable")
@staticmethod
def compute_checksum(data: bytes) -> bytes:
"""
@brief Compute the SHA-256 checksum of the given data.
@param data The data to compute the checksum for.
@return The SHA-256 checksum.
"""
return hashlib.sha256(data).digest()
def set_version(self, version: int) -> int:
"""
@brief Set the version of the OPAT file.
@param version The version to set.
@return The set version.
"""
self.header.version = version
return self.header.version
def set_source(self, source: str) -> str:
"""
@brief Set the source information of the OPAT file.
@param source The source information to set.
@return The set source information.
@throws TypeError if the source string is too long.
"""
if not self.validate_char_array_size(source, 64):
raise TypeError(f"sourceInfo string ({source}) is too long ({len(source)}). Max length is 64")
self.header.sourceInfo = source
return self.header.sourceInfo
def set_comment(self, comment: str) -> str:
"""
@brief Set the comment of the OPAT file.
@param comment The comment to set.
@return The set comment.
@throws TypeError if the comment string is too long.
"""
if not self.validate_char_array_size(comment, 128):
raise TypeError(f"comment string ({comment}) is too long ({len(comment)}). Max length is 128")
self.header.comment = comment
return self.header.comment
def add_table(self, X: float, Z: float, logR: Iterable[float], logT: Iterable[float], logKappa: Iterable[Iterable[float]]):
"""
@brief Add a table to the OPAT file.
@param X The X composition value.
@param Z The Z composition value.
@param logR The logR values.
@param logT The logT values.
@param logKappa The logKappa values.
@throws ValueError if logKappa is not a non-empty 2D array or if logR and logT are not 1D arrays.
"""
self.validate_logKappa(logKappa)
self.validate_1D(logR, "logR")
self.validate_1D(logT, "logT")
@@ -142,6 +201,10 @@ class OpatIO:
def _header_bytes(self) -> bytes:
"""
@brief Convert the header to bytes.
@return The header as bytes.
"""
headerBytes = struct.pack(
"<4s H I I Q 16s 64s 128s 26s",
self.header.magic.encode('utf-8'),
@@ -157,6 +220,11 @@ class OpatIO:
return headerBytes
def _table_bytes(self, table: OPATTable) -> Tuple[bytes, bytes]:
"""
@brief Convert a table to bytes.
@param table The OPAT table.
@return A tuple containing the checksum and the table as bytes.
"""
logR = table.logR.flatten()
logT = table.logT.flatten()
logKappa = table.logKappa.flatten()
@@ -172,6 +240,12 @@ class OpatIO:
return (checksum, tableBytes)
def _tableIndex_bytes(self, tableIndex: TableIndex) -> bytes:
"""
@brief Convert a table index to bytes.
@param tableIndex The table index.
@return The table index as bytes.
@throws RuntimeError if the table index entry does not have 64 bytes.
"""
tableIndexBytes = struct.pack(
'<ddQQ',
tableIndex.X,
@@ -187,8 +261,12 @@ class OpatIO:
return tableIndexBytes
def __repr__(self) -> str:
"""
@brief Get the string representation of the OpatIO object.
@return The string representation.
"""
reprString = f"""OpatIO(
versoion: {self.header.version}
version: {self.header.version}
numTables: {self.header.numTables}
headerSize: {self.header.headerSize}
indexOffset: {self.header.indexOffset}
@@ -200,12 +278,19 @@ class OpatIO:
return reprString
def _format_table_as_string(self, table: OPATTable, X: float, Z: float) -> str:
"""
@brief Format a table as a string.
@param table The OPAT table.
@param X The X composition value.
@param Z The Z composition value.
@return The formatted table as a string.
"""
tableString: List[str] = []
# fixed width X and Z header per table
tableString.append(f"X: {X:<10.4f} Z: {Z:<10.4f}")
tableString.append("-" * 80)
# write logR accross the top (reserving one col for where logT will be)
logRRow = f"{"":<10}"
# write logR across the top (reserving one col for where logT will be)
logRRow = f"{'':<10}"
logRRowTrue = "".join(f"{r:<10.4f}" for r in table.logR)
tableString.append(logRRow + logRRowTrue)
for i, logT in enumerate(table.logT):
@@ -218,6 +303,11 @@ class OpatIO:
@staticmethod
def print_table_indexes(table_indexes: List[TableIndex]) -> str:
"""
@brief Print the table indexes.
@param table_indexes The list of table indexes.
@return The formatted table indexes as a string.
"""
if not table_indexes:
print("No table indexes found.")
return
@@ -231,6 +321,11 @@ class OpatIO:
return '\n'.join(tableRows)
def save_as_ascii(self, filename: str) -> str:
"""
@brief Save the OPAT file as an ASCII file.
@param filename The name of the file.
@return The name of the saved file.
"""
numericFMT = "{:.18e}"
currentStartByte: int = 256
tableIndexs: List[bytes] = []
@@ -268,6 +363,12 @@ class OpatIO:
f.write(self.print_table_indexes(tableIndexs))
def save(self, filename: str) -> str:
"""
@brief Save the OPAT file as a binary file.
@param filename The name of the file.
@return The name of the saved file.
@throws RuntimeError if the header does not have 256 bytes.
"""
tempHeaderBytes = self._header_bytes()
if len(tempHeaderBytes) != 256:
@@ -305,6 +406,12 @@ class OpatIO:
def loadOpat(filename: str) -> OpatIO:
"""
@brief Load an OPAT file.
@param filename The name of the file.
@return The loaded OpatIO object.
@throws RuntimeError if the header does not have 256 bytes.
"""
opat = OpatIO()
with open(filename, 'rb') as f:
headerBytes: bytes = f.read(256)
@@ -355,4 +462,3 @@ def loadOpat(filename: str) -> OpatIO:
opat.add_table(tableIndex.X, tableIndex.Z, logR, logT, logKappa)
return opat