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aq-nwb 0.1.0 +
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@@ -100,7 +100,7 @@
-
docs/pages/about.dox File Reference
+
docs/pages/2_devdocs.dox File Reference
@@ -108,8 +108,8 @@ diff --git a/_base_i_o_8cpp.html b/_base_i_o_8cpp.html index 92a15883..b5cd8cd6 100644 --- a/_base_i_o_8cpp.html +++ b/_base_i_o_8cpp.html @@ -4,7 +4,7 @@ - + aq-nwb: src/BaseIO.cpp File Reference @@ -39,7 +39,7 @@ - + @@ -166,8 +167,8 @@ var sectionId = 'dynsection-1'; Node2->Node3 - - + + @@ -202,8 +203,8 @@ var sectionId = 'dynsection-1'; Node2->Node6 - - + + @@ -402,7 +403,7 @@ var sectionId = 'dynsection-1'; Node4->Node6 - + diff --git a/_types_8hpp__dep__incl_org.svg b/_types_8hpp__dep__incl_org.svg index cfef7f1e..bd2153ae 100644 --- a/_types_8hpp__dep__incl_org.svg +++ b/_types_8hpp__dep__incl_org.svg @@ -1,11 +1,11 @@ - - + src/Types.hpp @@ -120,8 +120,8 @@ Node2->Node3 - - + + @@ -156,8 +156,8 @@ Node2->Node6 - - + + @@ -356,7 +356,7 @@ Node4->Node6 - + diff --git a/_types_8hpp__incl.svg b/_types_8hpp__incl.svg index 7c5d0bbb..5a0aab2b 100644 --- a/_types_8hpp__incl.svg +++ b/_types_8hpp__incl.svg @@ -1,13 +1,14 @@ - - + + + + + +docs/pages/devdocs + +clusterdir_ef3b2545113449f8f25e623a543d64e3 + + +pages + + + + + +dir_30843f9e2f8f173fdeb0362489290dc6 + + +devdocs + + + + + + + + + + diff --git a/dir_30843f9e2f8f173fdeb0362489290dc6_dep_org.svg b/dir_30843f9e2f8f173fdeb0362489290dc6_dep_org.svg new file mode 100644 index 00000000..e38267e8 --- /dev/null +++ b/dir_30843f9e2f8f173fdeb0362489290dc6_dep_org.svg @@ -0,0 +1,29 @@ + + + + + + +docs/pages/devdocs + +clusterdir_ef3b2545113449f8f25e623a543d64e3 + + +pages + + + + + +dir_30843f9e2f8f173fdeb0362489290dc6 + + +devdocs + + + + + diff --git a/dir_3875c1e54b4d5fadc95eea4e5fdc191f.html b/dir_3875c1e54b4d5fadc95eea4e5fdc191f.html index cb3b4dad..a6085574 100644 --- a/dir_3875c1e54b4d5fadc95eea4e5fdc191f.html +++ b/dir_3875c1e54b4d5fadc95eea4e5fdc191f.html @@ -4,7 +4,7 @@ - + aq-nwb: src/nwb Directory Reference @@ -39,7 +39,7 @@ - + + + + + + + + + + + + + + + + +
+
+ + + + + + + +
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aq-nwb 0.1.0 +
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HDF5 I/O
+
+
+

+Chunking

+

For datasets intended for recording, AqNWB uses chunking to ensure the dataset can be extended as new data arrives during the recording process. Using chunking in HDF5, a dataset is divided into fixed-size blocks (called chunks), which are stored separately in the file. This technique is particularly beneficial for large datasets and offers several advantages:

+
    +
  • Extend datasets: Chunked datasets can be easily extended in any dimension. This flexibility is crucial for recording datasets where the size of the dataset is not known in advance.
    • +
  • Performance Optimization: By carefully choosing the chunk size, you can optimize performance based on your particular read/write access patterns. When only a portion of a chunked dataset is accessed, only the relevant chunks are read or written, reducing the amount of I/O operations.
    • +
  • Compression: Data within each chunk can be compressed independently, which can help to significant reduce data size, especially for datasets with redundancy.
    • +
+
Warning
Choosing a chunking configuration that does not align well with the desired read/write pattern may lead to reduced performance due to repeated read, decompression, and update to the same chunk or read of extra data as chunks are always read fully.
+
+
+

+Single-Writer Multiple-Reader (SWMR) Mode

+

The HDF5IO I/O backend uses by default SWMR mode while recording data. Using SWMR, one process can write to the HDF5 file and multiple other processes can read from the file concurrently while ensuring that the readers see a consistent view of the data.

+
+
+

+Why does AqNWB use SMWR mode?

+

Using SWMR has several key advantages for data acquisition applications:

+
    +
  • Concurrent Access: Enables one writer process to update the file while multiple reader processes read from it without blocking each other.
    • +
  • Data Consistency and Integrity: Ensures that readers see a consistent view of the data, even as it is being written. Readers will only see data that has been completely written and flushed to disk. Hence, SWMR mode, maintains the integrity and consistency of the data, ensuring that the HDF5 file remains readable even if errors should occur during the data acquisition process.
    • +
  • Real-Time Data Access: Useful for applications that need to monitor and analyze data in real-time as it is being generated.
    • +
  • Simplified Workflow for Real Time Analyses: Simplifies the architecture of applications that require real-time data consumption during acquisition, avoiding the need for intermediate storage solutions and complex inter-process communication or file locking mechanisms.
    • +
+
Note
While SWMR mode ensures data integrity, some data loss may still occur if the application crashes. Only data that has been completely written and flushed to disk will be readable. To manually flush data to disk use HDF5IO::flush.
+

+Writing an NWB file with SWMR mode

+

SWMR mode is enabled when calling HDF5IO::startRecording. Once SWMR mode is enabled, no new data objects (Datasets, Groups, Attributes etc.) can be created, but we can only add and set values to existing data objects. Since other processes may read from the HDF5 file, it is not possible to intermittently disable SWMR mode to add new objects, i.e., once SWMR mode is enabled, the only way to add new objects to the file is to close the file and reopen in read/write mode. As such, the typical workflow when using SWMR mode during data acquisition is to:

+
    +
  1. Open the HDF5 file
    2. +
  2. Create all elements of the NWB file
    3. +
  3. Start the recording process
    4. +
  4. Stop recording and close the file
    5. +
+

This workflow is applicable to a wide range of data acquisition use-cases. However, for use cases that require creation of new Groups and Datasets during acquisition, you can disable the use of SWMR mode by setting disableSWMRMode=true when constructing the AQNWB::HDF5::HDF5IO object.

+
Warning
While disabling SWMR mode allows Groups and Datasets to be created during and after recording, this comes at the cost of losing the concurrent access and data integrity features that SWMR mode provides.
+

+Code Examples

+

This code snippet shows all the includes that are being used by the code examples shown in this section:

+
#include <filesystem>
+
#include <future>
+
#include <iostream>
+
#include <memory>
+
#include <numeric>
+
#include <vector>
+
+
#include <catch2/catch_test_macros.hpp>
+
+
#include "hdf5/HDF5IO.hpp"
+
#include "nwb/NWBFile.hpp"
+
#include "nwb/file/ElectrodeTable.hpp"
+
#include "testUtils.hpp"
+
+
using namespace AQNWB;
+
namespace fs = std::filesystem;
+

+Workflow with SWMR

+
// create and open the HDF5 file. SWMR mode is used by default
+
std::string path = getTestFilePath("testWithSWMRMode.h5");
+
std::unique_ptr<HDF5::HDF5IO> hdf5io = std::make_unique<HDF5::HDF5IO>(path);
+
hdf5io->open();
+
+
// add a dataset
+
std::vector<int> testData(10000);
+
std::iota(testData.begin(), testData.end(), 1); // Initialize testData
+
std::string dataPath = "/data";
+
SizeType numBlocks = 10; // write 10 chunks of
+
SizeType numSamples = testData.size();
+
std::unique_ptr<BaseRecordingData> dataset = hdf5io->createArrayDataSet(
+
BaseDataType::I32, // type
+
SizeArray {0}, // size. Initial size of the dataset
+
SizeArray {1000}, // chunking. Size of a data chunk
+
dataPath); // path. Path to the dataset in the HDF5 file
+
+
// Start recording. Starting the recording places the HDF5 file in SWMR mode
+
Status status = hdf5io->startRecording();
+
REQUIRE(status == Status::Success);
+
+
// Once in SWMR mode we can add data to the file but we can no longer create
+
// new data objects (Groups, Datasets, Attributes etc.).
+
REQUIRE(hdf5io->canModifyObjects() == false);
+
+
// write the our testData to the file.
+
for (SizeType b = 0; b <= numBlocks; b++) {
+
// write a single 1D block of data and flush to file
+
std::vector<SizeType> dataShape = {numSamples};
+
dataset->writeDataBlock(dataShape, BaseDataType::I32, &testData[0]);
+
// Optionally we can flush all data to disk
+
status = hdf5io->flush();
+
REQUIRE(status == Status::Success);
+
}
+
+
// stop recording. In SWMR mode the file is now closed and recording cannot
+
// be restarted
+
status = hdf5io->stopRecording();
+
REQUIRE(hdf5io->isOpen() == false);
+
REQUIRE(hdf5io->startRecording() == Status::Failure);
+

+Workflow with SWMR disabled

+
// create and open the HDF5 file. With SWMR mode explicitly disabled
+
std::string path = getTestFilePath("testWithoutSWMRMode.h5");
+
std::unique_ptr<HDF5::HDF5IO> hdf5io =
+
std::make_unique<HDF5::HDF5IO>(path,
+
true // Disable SWMR mode
+
);
+
hdf5io->open();
+
+
// add a dataset
+
std::vector<int> testData(10000);
+
std::iota(testData.begin(), testData.end(), 1); // Initialize testData
+
std::string dataPath = "/data";
+
SizeType numBlocks = 10; // write 10 chunks of
+
SizeType numSamples = testData.size();
+
std::unique_ptr<BaseRecordingData> dataset = hdf5io->createArrayDataSet(
+
BaseDataType::I32, // type
+
SizeArray {0}, // size. Initial size of the dataset
+
SizeArray {1000}, // chunking. Size of a data chunk
+
dataPath); // path. Path to the dataset in the HDF5 file
+
+
// Start recording. Starting the recording places the HDF5 file in SWMR mode
+
Status status = hdf5io->startRecording();
+
REQUIRE(status == Status::Success);
+
+
// With SWMR mode disabled we are still allowed to create new data objects
+
// (Groups, Datasets, Attributes etc.) during the recording. However, with
+
// SWMR mode disabled, we lose the data consistency and concurrent read
+
// features that SWMR mode provides.
+
REQUIRE(hdf5io->canModifyObjects() == true);
+
+
// write the our testData to the file.
+
for (SizeType b = 0; b <= numBlocks; b++) {
+
// write a single 1D block of data and flush to file
+
std::vector<SizeType> dataShape = {numSamples};
+
dataset->writeDataBlock(dataShape, BaseDataType::I32, &testData[0]);
+
// Optionally we can flush all data to disk
+
status = hdf5io->flush();
+
REQUIRE(status == Status::Success);
+
}
+
+
// stop recording.
+
status = hdf5io->stopRecording();
+
+
// Since SWMR mode is disabled, stopping the recording won't close the file
+
// so that we can restart the recording if we want to
+
REQUIRE(hdf5io->isOpen() == true);
+
+
// Restart the recording
+
REQUIRE(hdf5io->startRecording() == Status::Success);
+
+
// Stop the recording and close the file
+
hdf5io->stopRecording();
+
hdf5io->close();
+
REQUIRE(hdf5io->isOpen() == false);
+

+Reading with SWMR mode

+

While the file is being written to in SWMR mode, readers must open the file with the H5F_ACC_RDONLY flag and then enable SWMR read mode using the H5Fstart_swmr_read function, e.g.:

+
hid_t file_id = H5Fopen("example.h5", H5F_ACC_RDONLY, H5P_DEFAULT);
+
H5Fstart_swmr_read(file_id);
+
+
+
+ + + + diff --git a/hdf5io_8dox.html b/hdf5io_8dox.html new file mode 100644 index 00000000..491951e0 --- /dev/null +++ b/hdf5io_8dox.html @@ -0,0 +1,116 @@ + + + + + + + + +aq-nwb: docs/pages/userdocs/hdf5io.dox File Reference + + + + + + + + + + + + + + + + + +
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Installing AqNWB
+
+
+

+Requirements

+

Please ensure that the required libraries described in the Requirements section are installed.

+

+Build

+

Here are the steps for building in release mode with a multi-configuration generator:

+
cmake -S . -B build
+
cmake --build build --config Release
+
Note
If you are using custom installations of HDF5 or BOOST that are not being detected automatically by cmake, you can specify HDF5_ROOT and BOOST_ROOT environment variables to point to install directories of HDF5 and BOOST respectively.
+

+Install

+

Here is the command for installing the release mode artifacts with a multi-configuration generator:

+
cmake --install build --config Release
+
+
+
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element}};$.powerTip.showTip=$.powerTip.show;$.powerTip.closeTip=$.powerTip.hide;function CSSCoordinates(){var me=this;me.top="auto";me.left="auto";me.right="auto";me.bottom="auto";me.set=function(property,value){if($.isNumeric(value)){me[property]=Math.round(value)}}}function DisplayController(element,options,tipController){var hoverTimer=null,myCloseDelay=null;function openTooltip(immediate,forceOpen){cancelTimer();if(!element.data(DATA_HASACTIVEHOVER)){if(!immediate){session.tipOpenImminent=true;hoverTimer=setTimeout(function intentDelay(){hoverTimer=null;checkForIntent()},options.intentPollInterval)}else{if(forceOpen){element.data(DATA_FORCEDOPEN,true)} +closeAnyDelayed();tipController.showTip(element)}}else{cancelClose()}}function closeTooltip(disableDelay){if(myCloseDelay){myCloseDelay=session.closeDelayTimeout=clearTimeout(myCloseDelay);session.delayInProgress=false}cancelTimer();session.tipOpenImminent=false;if(element.data(DATA_HASACTIVEHOVER)){element.data(DATA_FORCEDOPEN,false);if(!disableDelay){session.delayInProgress=true;session.closeDelayTimeout=setTimeout(function closeDelay(){session.closeDelayTimeout=null;tipController.hideTip(element);session.delayInProgress=false;myCloseDelay=null},options.closeDelay);myCloseDelay=session.closeDelayTimeout}else{tipController.hideTip(element)}}}function checkForIntent(){var xDifference=Math.abs(session.previousX-session.currentX),yDifference=Math.abs(session.previousY-session.currentY),totalDifference=xDifference+yDifference;if(totalDifference",{id:options.popupId});if($body.length===0){$body=$("body")}$body.append(tipElement);session.tooltips=session.tooltips?session.tooltips.add(tipElement):tipElement}if(options.followMouse){if(!tipElement.data(DATA_HASMOUSEMOVE)){$document.on("mousemove"+EVENT_NAMESPACE,positionTipOnCursor);$window.on("scroll"+EVENT_NAMESPACE,positionTipOnCursor);tipElement.data(DATA_HASMOUSEMOVE,true)}}function beginShowTip(element){element.data(DATA_HASACTIVEHOVER,true);tipElement.queue(function queueTipInit(next){showTip(element);next()})}function showTip(element){var tipContent;if(!element.data(DATA_HASACTIVEHOVER)){return}if( +session.isTipOpen){if(!session.isClosing){hideTip(session.activeHover)}tipElement.delay(100).queue(function queueTipAgain(next){showTip(element);next()});return}element.trigger("powerTipPreRender");tipContent=getTooltipContent(element);if(tipContent){tipElement.empty().append(tipContent)}else{return}element.trigger("powerTipRender");session.activeHover=element;session.isTipOpen=true;tipElement.data(DATA_MOUSEONTOTIP,options.mouseOnToPopup);tipElement.addClass(options.popupClass);if(!options.followMouse||element.data(DATA_FORCEDOPEN)){positionTipOnElement(element);session.isFixedTipOpen=true}else{positionTipOnCursor()}if(!element.data(DATA_FORCEDOPEN)&&!options.followMouse){$document.on("click"+EVENT_NAMESPACE,function documentClick(event){var target=event.target;if(target!==element[0]){if(options.mouseOnToPopup){if(target!==tipElement[0]&&!$.contains(tipElement[0],target)){$.powerTip.hide()}}else{$.powerTip.hide()}}})}if(options.mouseOnToPopup&&!options.manual){tipElement.on("mouseenter"+EVENT_NAMESPACE, +function tipMouseEnter(){if(session.activeHover){session.activeHover.data(DATA_DISPLAYCONTROLLER).cancel()}});tipElement.on("mouseleave"+EVENT_NAMESPACE,function tipMouseLeave(){if(session.activeHover){session.activeHover.data(DATA_DISPLAYCONTROLLER).hide()}})}tipElement.fadeIn(options.fadeInTime,function fadeInCallback(){if(!session.desyncTimeout){session.desyncTimeout=setInterval(closeDesyncedTip,500)}element.trigger("powerTipOpen")})}function hideTip(element){session.isClosing=true;session.isTipOpen=false;session.desyncTimeout=clearInterval(session.desyncTimeout);element.data(DATA_HASACTIVEHOVER,false);element.data(DATA_FORCEDOPEN,false);$document.off("click"+EVENT_NAMESPACE);tipElement.off(EVENT_NAMESPACE);tipElement.fadeOut(options.fadeOutTime,function fadeOutCallback(){var coords=new 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getViewportDimensions(){session.scrollLeft=$window.scrollLeft();session.scrollTop=$window.scrollTop();session.windowWidth=$window.width();session.windowHeight=$window.height()}function trackResize(){session.windowWidth=$window.width();session.windowHeight=$window.height()}function trackScroll(){var x=$window.scrollLeft(),y=$window.scrollTop();if(x!==session.scrollLeft){session.currentX+=x-session.scrollLeft;session.scrollLeft=x}if(y!==session.scrollTop){session.currentY+=y-session.scrollTop;session.scrollTop=y}}function trackMouse(event){session.currentX=event.pageX;session.currentY=event.pageY}function isMouseOver(element){var elementPosition=element.offset(),elementBox=element[0].getBoundingClientRect(), +elementWidth=elementBox.right-elementBox.left,elementHeight=elementBox.bottom-elementBox.top;return session.currentX>=elementPosition.left&&session.currentX<=elementPosition.left+elementWidth&&session.currentY>=elementPosition.top&&session.currentY<=elementPosition.top+elementHeight}function getTooltipContent(element){var tipText=element.data(DATA_POWERTIP),tipObject=element.data(DATA_POWERTIPJQ),tipTarget=element.data(DATA_POWERTIPTARGET),targetElement,content;if(tipText){if($.isFunction(tipText)){tipText=tipText.call(element[0])}content=tipText}else if(tipObject){if($.isFunction(tipObject)){tipObject=tipObject.call(element[0])}if(tipObject.length>0){content=tipObject.clone(true,true)}}else if(tipTarget){targetElement=$("#"+tipTarget);if(targetElement.length>0){content=targetElement.html()}}return content}function getViewportCollisions(coords,elementWidth,elementHeight){var viewportTop=session.scrollTop,viewportLeft=session.scrollLeft,viewportBottom=viewportTop+session.windowHeight, 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e=t.dataSM("parent-a"),i=this.isCollapsible();if((this.opts.keepHighlighted||i)&&e.addClass("highlighted"),i)t.removeClass("sm-nowrap").css({zIndex:"",width:"auto",minWidth:"",maxWidth:"",top:"",left:"",marginLeft:"",marginTop:""});else{if(t.css("z-index",this.zIndexInc=(this.zIndexInc||this.getStartZIndex())+1),(this.opts.subMenusMinWidth||this.opts.subMenusMaxWidth)&&(t.css({width:"auto",minWidth:"",maxWidth:""}).addClass("sm-nowrap"),this.opts.subMenusMinWidth&&t.css("min-width",this.opts.subMenusMinWidth),this.opts.subMenusMaxWidth)){var s=this.getWidth(t);t.css("max-width",this.opts.subMenusMaxWidth),s>this.getWidth(t)&&t.removeClass("sm-nowrap").css("width",this.opts.subMenusMaxWidth)}this.menuPosition(t)}var 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define&&define.amd?define(["jquery"],t):"object"==typeof module&&"object"==typeof module.exports?module.exports=t(require("jquery")):t(jQuery)})(function($){function initMouseDetection(t){var e=".smartmenus_mouse";if(mouseDetectionEnabled||t)mouseDetectionEnabled&&t&&($(document).off(e),mouseDetectionEnabled=!1);else{var i=!0,s=null,o={mousemove:function(t){var e={x:t.pageX,y:t.pageY,timeStamp:(new Date).getTime()};if(s){var o=Math.abs(s.x-e.x),a=Math.abs(s.y-e.y);if((o>0||a>0)&&2>=o&&2>=a&&300>=e.timeStamp-s.timeStamp&&(mouse=!0,i)){var n=$(t.target).closest("a");n.is("a")&&$.each(menuTrees,function(){return $.contains(this.$root[0],n[0])?(this.itemEnter({currentTarget:n[0]}),!1):void 0}),i=!1}}s=e}};o[touchEvents?"touchstart":"pointerover pointermove pointerout MSPointerOver MSPointerMove MSPointerOut"]=function(t){isTouchEvent(t.originalEvent)&&(mouse=!1)},$(document).on(getEventsNS(o,e)), +mouseDetectionEnabled=!0}}function isTouchEvent(t){return!/^(4|mouse)$/.test(t.pointerType)}function getEventsNS(t,e){e||(e="");var i={};for(var s in t)i[s.split(" ").join(e+" ")+e]=t[s];return i}var menuTrees=[],mouse=!1,touchEvents="ontouchstart"in window,mouseDetectionEnabled=!1,requestAnimationFrame=window.requestAnimationFrame||function(t){return setTimeout(t,1e3/60)},cancelAnimationFrame=window.cancelAnimationFrame||function(t){clearTimeout(t)},canAnimate=!!$.fn.animate;return $.SmartMenus=function(t,e){this.$root=$(t),this.opts=e,this.rootId="",this.accessIdPrefix="",this.$subArrow=null,this.activatedItems=[],this.visibleSubMenus=[],this.showTimeout=0,this.hideTimeout=0,this.scrollTimeout=0,this.clickActivated=!1,this.focusActivated=!1,this.zIndexInc=0,this.idInc=0,this.$firstLink=null,this.$firstSub=null,this.disabled=!1,this.$disableOverlay=null,this.$touchScrollingSub=null,this.cssTransforms3d="perspective"in t.style||"webkitPerspective"in t.style,this.wasCollapsible=!1,this.init()},$.extend( 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s=/(index|default)\.[^#\?\/]*/i,o=/#.*/,a=window.location.href.replace(s,""),n=a.replace(o,"");this.$root.find("a").each(function(){var t=this.href.replace(s,""),i=$(this);(t==a||t==n)&&(i.addClass("current"),e.opts.markCurrentTree&&i.parentsUntil("[data-smartmenus-id]","ul").each(function(){$(this).dataSM("parent-a").addClass("current")}))})}this.wasCollapsible=this.isCollapsible()},destroy:function(t){if(!t){var e=".smartmenus";this.$root.removeData( +"smartmenus").removeAttr("data-smartmenus-id").removeDataSM("level").off(e),e+=this.rootId,$(document).off(e),$(window).off(e),this.opts.subIndicators&&(this.$subArrow=null)}this.menuHideAll();var i=this;this.$root.find("ul").each(function(){var t=$(this);t.dataSM("scroll-arrows")&&t.dataSM("scroll-arrows").remove(),t.dataSM("shown-before")&&((i.opts.subMenusMinWidth||i.opts.subMenusMaxWidth)&&t.css({width:"",minWidth:"",maxWidth:""}).removeClass("sm-nowrap"),t.dataSM("scroll-arrows")&&t.dataSM("scroll-arrows").remove(),t.css({zIndex:"",top:"",left:"",marginLeft:"",marginTop:"",display:""})),0==(t.attr("id")||"").indexOf(i.accessIdPrefix)&&t.removeAttr("id")}).removeDataSM("in-mega").removeDataSM("shown-before").removeDataSM("scroll-arrows").removeDataSM("parent-a").removeDataSM("level").removeDataSM("beforefirstshowfired").removeAttr("role").removeAttr("aria-hidden").removeAttr("aria-labelledby").removeAttr("aria-expanded"),this.$root.find("a.has-submenu").each(function(){var t=$(this);0==t.attr("id" +).indexOf(i.accessIdPrefix)&&t.removeAttr("id")}).removeClass("has-submenu").removeDataSM("sub").removeAttr("aria-haspopup").removeAttr("aria-controls").removeAttr("aria-expanded").closest("li").removeDataSM("sub"),this.opts.subIndicators&&this.$root.find("span.sub-arrow").remove(),this.opts.markCurrentItem&&this.$root.find("a.current").removeClass("current"),t||(this.$root=null,this.$firstLink=null,this.$firstSub=null,this.$disableOverlay&&(this.$disableOverlay.remove(),this.$disableOverlay=null),menuTrees.splice($.inArray(this,menuTrees),1))},disable:function(t){if(!this.disabled){if(this.menuHideAll(),!t&&!this.opts.isPopup&&this.$root.is(":visible")){var e=this.$root.offset();this.$disableOverlay=$('
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e=t.originalEvent.touches[0];this.lastTouch.x2=e.pageX,this.lastTouch.y2=e.pageY}},docTouchStart:function(t){var e=t.originalEvent.touches[0];this.lastTouch={x1:e.pageX,y1:e.pageY,target:e.target}},enable:function(){this.disabled&&(this.$disableOverlay&&(this.$disableOverlay.remove(),this.$disableOverlay=null),this.disabled=!1)},getClosestMenu:function(t){for( +var e=$(t).closest("ul");e.dataSM("in-mega");)e=e.parent().closest("ul");return e[0]||null},getHeight:function(t){return this.getOffset(t,!0)},getOffset:function(t,e){var i;"none"==t.css("display")&&(i={position:t[0].style.position,visibility:t[0].style.visibility},t.css({position:"absolute",visibility:"hidden"}).show());var s=t[0].getBoundingClientRect&&t[0].getBoundingClientRect(),o=s&&(e?s.height||s.bottom-s.top:s.width||s.right-s.left);return o||0===o||(o=e?t[0].offsetHeight:t[0].offsetWidth),i&&t.hide().css(i),o},getStartZIndex:function(t){var 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0}),t},isLinkInMegaMenu:function(t){return $(this.getClosestMenu(t[0])).hasClass("mega-menu")},isTouchMode:function(){return!mouse||this.opts.noMouseOver||this.isCollapsible()},itemActivate:function(t,e){var i=t.closest("ul"),s=i.dataSM("level");if(s>1&&(!this.activatedItems[s-2]||this.activatedItems[s-2][0]!=i.dataSM("parent-a")[0])){var o=this;$(i.parentsUntil("[data-smartmenus-id]","ul").get().reverse()).add(i).each(function(){o.itemActivate($(this).dataSM("parent-a"))})}if(( +!this.isCollapsible()||e)&&this.menuHideSubMenus(this.activatedItems[s-1]&&this.activatedItems[s-1][0]==t[0]?s:s-1),this.activatedItems[s-1]=t,this.$root.triggerHandler("activate.smapi",t[0])!==!1){var a=t.dataSM("sub");a&&(this.isTouchMode()||!this.opts.showOnClick||this.clickActivated)&&this.menuShow(a)}},itemBlur:function(t){var e=$(t.currentTarget);this.handleItemEvents(e)&&this.$root.triggerHandler("blur.smapi",e[0])},itemClick:function(t){var e=$(t.currentTarget);if(this.handleItemEvents(e)){if(this.$touchScrollingSub&&this.$touchScrollingSub[0]==e.closest("ul")[0])return this.$touchScrollingSub=null,t.stopPropagation(),!1;if(this.$root.triggerHandler("click.smapi",e[0])===!1)return!1;var i=$(t.target).is(".sub-arrow"),s=e.dataSM("sub"),o=s?2==s.dataSM("level"):!1,a=this.isCollapsible(),n=/toggle$/.test(this.opts.collapsibleBehavior),r=/link$/.test(this.opts.collapsibleBehavior),h=/^accordion/.test(this.opts.collapsibleBehavior);if(s&&!s.is(":visible")){if((!r||!a||i)&&(this.opts.showOnClick&&o&&( +this.clickActivated=!0),this.itemActivate(e,h),s.is(":visible")))return this.focusActivated=!0,!1}else if(a&&(n||i))return this.itemActivate(e,h),this.menuHide(s),n&&(this.focusActivated=!1),!1;return this.opts.showOnClick&&o||e.hasClass("disabled")||this.$root.triggerHandler("select.smapi",e[0])===!1?!1:void 0}},itemDown:function(t){var e=$(t.currentTarget);this.handleItemEvents(e)&&e.dataSM("mousedown",!0)},itemEnter:function(t){var e=$(t.currentTarget);if(this.handleItemEvents(e)){if(!this.isTouchMode()){this.showTimeout&&(clearTimeout(this.showTimeout),this.showTimeout=0);var i=this;this.showTimeout=setTimeout(function(){i.itemActivate(e)},this.opts.showOnClick&&1==e.closest("ul").dataSM("level")?1:this.opts.showTimeout)}this.$root.triggerHandler("mouseenter.smapi",e[0])}},itemFocus:function(t){var e=$(t.currentTarget);this.handleItemEvents(e)&&(!this.focusActivated||this.isTouchMode()&&e.dataSM("mousedown")||this.activatedItems.length&&this.activatedItems[this.activatedItems.length-1][0]==e[0 +]||this.itemActivate(e,!0),this.$root.triggerHandler("focus.smapi",e[0]))},itemLeave:function(t){var e=$(t.currentTarget);this.handleItemEvents(e)&&(this.isTouchMode()||(e[0].blur(),this.showTimeout&&(clearTimeout(this.showTimeout),this.showTimeout=0)),e.removeDataSM("mousedown"),this.$root.triggerHandler("mouseleave.smapi",e[0]))},menuHide:function(t){if(this.$root.triggerHandler("beforehide.smapi",t[0])!==!1&&(canAnimate&&t.stop(!0,!0),"none"!=t.css("display"))){var e=function(){t.css("z-index","")};this.isCollapsible()?canAnimate&&this.opts.collapsibleHideFunction?this.opts.collapsibleHideFunction.call(this,t,e):t.hide(this.opts.collapsibleHideDuration,e):canAnimate&&this.opts.hideFunction?this.opts.hideFunction.call(this,t,e):t.hide(this.opts.hideDuration,e),t.dataSM("scroll")&&(this.menuScrollStop(t),t.css({"touch-action":"","-ms-touch-action":"","-webkit-transform":"",transform:""}).off(".smartmenus_scroll").removeDataSM("scroll").dataSM("scroll-arrows").hide()),t.dataSM("parent-a").removeClass( 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i=this.activatedItems[e].dataSM("sub");i&&this.menuHide(i)}},menuInit:function(t){if(!t.dataSM("in-mega")){ +t.hasClass("mega-menu")&&t.find("ul").dataSM("in-mega",!0);for(var e=2,i=t[0];(i=i.parentNode.parentNode)!=this.$root[0];)e++;var s=t.prevAll("a").eq(-1);s.length||(s=t.prevAll().find("a").eq(-1)),s.addClass("has-submenu").dataSM("sub",t),t.dataSM("parent-a",s).dataSM("level",e).parent().dataSM("sub",t);var o=s.attr("id")||this.accessIdPrefix+ ++this.idInc,a=t.attr("id")||this.accessIdPrefix+ ++this.idInc;s.attr({id:o,"aria-haspopup":"true","aria-controls":a,"aria-expanded":"false"}),t.attr({id:a,role:"group","aria-hidden":"true","aria-labelledby":o,"aria-expanded":"false"}),this.opts.subIndicators&&s[this.opts.subIndicatorsPos](this.$subArrow.clone())}},menuPosition:function(t){var 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e=t.dataSM("scroll"),i=$(window).scrollTop()-t.dataSM("parent-a").offset().top-e.itemH;this.cssTransforms3d&&(i=-(parseFloat(t.css("margin-top"))-i)),$.extend(e,{upEnd:i, +downEnd:i+this.getViewportHeight()-e.subH})},menuScrollStop:function(t){return this.scrollTimeout?(cancelAnimationFrame(this.scrollTimeout),this.scrollTimeout=0,t.dataSM("scroll").step=1,!0):void 0},menuScrollTouch:function(t,e){if(e=e.originalEvent,isTouchEvent(e)){var i=this.getTouchPoint(e);if(this.getClosestMenu(i.target)==t[0]){var s=t.dataSM("scroll");if(/(start|down)$/i.test(e.type))this.menuScrollStop(t)?(e.preventDefault(),this.$touchScrollingSub=t):this.$touchScrollingSub=null,this.menuScrollRefreshData(t),$.extend(s,{touchStartY:i.pageY,touchStartTime:e.timeStamp});else if(/move$/i.test(e.type)){var o=void 0!==s.touchY?s.touchY:s.touchStartY;if(void 0!==o&&o!=i.pageY){this.$touchScrollingSub=t;var a=i.pageY>o;void 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e=t.dataSM("parent-a"),i=this.isCollapsible();if((this.opts.keepHighlighted||i)&&e.addClass("highlighted"),i)t.removeClass("sm-nowrap").css({zIndex:"",width:"auto",minWidth:"",maxWidth:"",top:"",left:"",marginLeft:"",marginTop:""});else{if(t.css("z-index",this.zIndexInc=(this.zIndexInc||this.getStartZIndex())+1),(this.opts.subMenusMinWidth||this.opts.subMenusMaxWidth)&&(t.css({width:"auto",minWidth:"",maxWidth:""}).addClass("sm-nowrap"),this.opts.subMenusMinWidth&&t.css("min-width",this.opts.subMenusMinWidth),this.opts.subMenusMaxWidth)){var s=this.getWidth(t);t.css("max-width",this.opts.subMenusMaxWidth),s>this.getWidth(t +)&&t.removeClass("sm-nowrap").css("width",this.opts.subMenusMaxWidth)}this.menuPosition(t)}var o=function(){t.css("overflow","")};i?canAnimate&&this.opts.collapsibleShowFunction?this.opts.collapsibleShowFunction.call(this,t,o):t.show(this.opts.collapsibleShowDuration,o):canAnimate&&this.opts.showFunction?this.opts.showFunction.call(this,t,o):t.show(this.opts.showDuration,o),e.attr("aria-expanded","true"),t.attr({"aria-expanded":"true","aria-hidden":"false"}),this.visibleSubMenus.push(t),this.$root.triggerHandler("show.smapi",t[0])}},popupHide:function(t){this.hideTimeout&&(clearTimeout(this.hideTimeout),this.hideTimeout=0);var e=this;this.hideTimeout=setTimeout(function(){e.menuHideAll()},t?1:this.opts.hideTimeout)},popupShow:function(t,e){if(!this.opts.isPopup)return alert('SmartMenus jQuery Error:\n\nIf you want to show this menu via the "popupShow" method, set the isPopup:true option.'),void 0;if(this.hideTimeout&&(clearTimeout(this.hideTimeout),this.hideTimeout=0),this.$root.dataSM("shown-before",!0), +canAnimate&&this.$root.stop(!0,!0),!this.$root.is(":visible")){this.$root.css({left:t,top:e});var i=this,s=function(){i.$root.css("overflow","")};canAnimate&&this.opts.showFunction?this.opts.showFunction.call(this,this.$root,s):this.$root.show(this.opts.showDuration,s),this.visibleSubMenus[0]=this.$root}},refresh:function(){this.destroy(!0),this.init(!0)},rootKeyDown:function(t){if(this.handleEvents())switch(t.keyCode){case 27:var e=this.activatedItems[0];if(e){this.menuHideAll(),e[0].focus();var i=e.dataSM("sub");i&&this.menuHide(i)}break;case 32:var s=$(t.target);if(s.is("a")&&this.handleItemEvents(s)){var i=s.dataSM("sub");i&&!i.is(":visible")&&(this.itemClick({currentTarget:t.target}),t.preventDefault())}}},rootOut:function(t){if(this.handleEvents()&&!this.isTouchMode()&&t.target!=this.$root[0]&&(this.hideTimeout&&(clearTimeout(this.hideTimeout),this.hideTimeout=0),!this.opts.showOnClick||!this.opts.hideOnClick)){var e=this;this.hideTimeout=setTimeout(function(){e.menuHideAll()},this.opts.hideTimeout)}}, +rootOver:function(t){this.handleEvents()&&!this.isTouchMode()&&t.target!=this.$root[0]&&this.hideTimeout&&(clearTimeout(this.hideTimeout),this.hideTimeout=0)},winResize:function(t){if(this.handleEvents()){if(!("onorientationchange"in window)||"orientationchange"==t.type){var e=this.isCollapsible();this.wasCollapsible&&e||(this.activatedItems.length&&this.activatedItems[this.activatedItems.length-1][0].blur(),this.menuHideAll()),this.wasCollapsible=e}}else if(this.$disableOverlay){var i=this.$root.offset();this.$disableOverlay.css({top:i.top,left:i.left,width:this.$root.outerWidth(),height:this.$root.outerHeight()})}}}}),$.fn.dataSM=function(t,e){return e?this.data(t+"_smartmenus",e):this.data(t+"_smartmenus")},$.fn.removeDataSM=function(t){return this.removeData(t+"_smartmenus")},$.fn.smartmenus=function(options){if("string"==typeof options){var args=arguments,method=options;return Array.prototype.shift.call(args),this.each(function(){var t=$(this).data("smartmenus");t&&t[method]&&t[method].apply(t,args)})} +return this.each(function(){var dataOpts=$(this).data("sm-options")||null;if(dataOpts)try{dataOpts=eval("("+dataOpts+")")}catch(e){dataOpts=null,alert('ERROR\n\nSmartMenus jQuery init:\nInvalid "data-sm-options" attribute value syntax.')}new $.SmartMenus(this,$.extend({},$.fn.smartmenus.defaults,options,dataOpts))})},$.fn.smartmenus.defaults={isPopup:!1,mainMenuSubOffsetX:0,mainMenuSubOffsetY:0,subMenusSubOffsetX:0,subMenusSubOffsetY:0,subMenusMinWidth:"10em",subMenusMaxWidth:"20em",subIndicators:!0,subIndicatorsPos:"append",subIndicatorsText:"",scrollStep:30,scrollAccelerate:!0,showTimeout:250,hideTimeout:500,showDuration:0,showFunction:null,hideDuration:0,hideFunction:function(t,e){t.fadeOut(200,e)},collapsibleShowDuration:0,collapsibleShowFunction:function(t,e){t.slideDown(200,e)},collapsibleHideDuration:0,collapsibleHideFunction:function(t,e){t.slideUp(200,e)},showOnClick:!1,hideOnClick:!0,noMouseOver:!1,keepInViewport:!0,keepHighlighted:!0,markCurrentItem:!1,markCurrentTree:!0,rightToLeftSubMenus:!1, +bottomToTopSubMenus:!1,collapsibleBehavior:"default"},$}); diff --git a/license_8dox.html b/license_8dox.html new file mode 100644 index 00000000..69a9a3e7 --- /dev/null +++ b/license_8dox.html @@ -0,0 +1,116 @@ + + + + + + + + +aq-nwb: docs/pages/devdocs/license.dox File Reference + + + + + + + + + + + + + + + + + +
+
+ + + + + + + +
+
aq-nwb 0.1.0 +
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docs/pages/devdocs/license.dox File Reference
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+
+
+
+ + + + diff --git a/license_page.html b/license_page.html new file mode 100644 index 00000000..f0a4e6c1 --- /dev/null +++ b/license_page.html @@ -0,0 +1,159 @@ + + + + + + + + +aq-nwb: License + + + + + + + + + + + + + + + + + +
+
+ + + + + + + +
+
aq-nwb 0.1.0 +
+
+
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License
+
+
+
AqNWB Copyright (c) 2024, The Regents of the University of California,
+
through Lawrence Berkeley National Laboratory (subject to receipt of any
+
required approvals from the U.S. Dept. of Energy). All rights reserved.
+
+
Redistribution and use in source and binary forms, with or without
+
modification, are permitted provided that the following conditions are met:
+
+
(1) Redistributions of source code must retain the above copyright notice,
+
this list of conditions and the following disclaimer.
+
+
(2) Redistributions in binary form must reproduce the above copyright
+
notice, this list of conditions and the following disclaimer in the
+
documentation and/or other materials provided with the distribution.
+
+
(3) Neither the name of the University of California, Lawrence Berkeley
+
National Laboratory, U.S. Dept. of Energy nor the names of its contributors
+
may be used to endorse or promote products derived from this software
+
without specific prior written permission.
+
+
+
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+
ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+
LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+
SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+
INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+
CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF
+
THE POSSIBILITY OF SUCH DAMAGE.
+
+
You are under no obligation whatsoever to provide any bug fixes, patches,
+
or upgrades to the features, functionality or performance of the source
+
code ("Enhancements") to anyone; however, if you choose to make your
+
Enhancements available either publicly, or directly to Lawrence Berkeley
+
National Laboratory, without imposing a separate written license agreement
+
for such Enhancements, then you hereby grant the following license: a
+
non-exclusive, royalty-free perpetual license to install, use, modify,
+
prepare derivative works, incorporate into other computer software,
+
distribute, and sublicense such enhancements or derivative works thereof,
+
in binary and source code form.
+
+
+
+ + + + diff --git a/namespace_a_q_n_w_b.html b/namespace_a_q_n_w_b.html index c3dc2b1c..4ac1bbdd 100644 --- a/namespace_a_q_n_w_b.html +++ b/namespace_a_q_n_w_b.html @@ -4,7 +4,7 @@ - + aq-nwb: AQNWB Namespace Reference @@ -39,7 +39,7 @@
- + + + + + + + + + + + + + + + + +
+
+ + + + + + + +
+
aq-nwb 0.1.0 +
+
+
+ + + + + + + + +
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+
Testing
+
+
+

+Unit Tests

+

AqNWB uses ctest and CATCH2 for unit testing. Relevant files for the unit tests are located at:

    +
  • /tests : Sources of the unit tests
    • +
  • /tests/examples : Sources of example code used in the docs. The examples are implemented like regular unit tests but their purpose is to provide examples for the docs (rather than testing specific cases) and as such commonly include Doxygen section markers to allow inclusion of sections of code in the Doxygen docs.
    • +
+

+Running Unit Tests

+

If you built AqNWB with the dev mode preset, then simply call:

+
ctest --preset=dev
+

Alternatively go to your build directory and run ctest directly, e.g.:

+
cd <my_build_dir>
+
ctest
+

+Spellcheck

+

AqNWB uses codespell to check the code for spelling errors. You can run the spellchecker via:

+
cmake --build --preset=dev --target=spell-check
+

To automatically fix spelling errors you can run codespell via the spell-fix target instead:

+
cmake --build --preset=dev --target=spell-fix
+
Note
codespell uses a relatively small dictionary of common misspellings and their corrections. For more comprehensive spellchecking (in particular of the documentation) additional spellchecking via more detailed spellcheckers (e.g., aspell) is recommended.
+

+Linting

+

AqNWB uses clang-format for linting the code. You can run the linter via:

+
cmake --build --preset=dev --target=format-check
+

To automatically fix formatting errors you can run the linter via the format-fix target instead:

cmake --build --preset=dev --target=format-fix
+
+
+
+ + + + diff --git a/testing_8dox.html b/testing_8dox.html new file mode 100644 index 00000000..87916ebf --- /dev/null +++ b/testing_8dox.html @@ -0,0 +1,116 @@ + + + + + + + + +aq-nwb: docs/pages/devdocs/testing.dox File Reference + + + + + + + + + + + + + + + + + +
+
+ + + + + + + +
+
aq-nwb 0.1.0 +
+
+
+ + + + + + + + +
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docs/pages/devdocs/testing.dox File Reference
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+
+
+
+ + + + diff --git a/about.html b/userdocs.html similarity index 86% rename from about.html rename to userdocs.html index 7ab92d91..6a66acbc 100644 --- a/about.html +++ b/userdocs.html @@ -4,9 +4,9 @@ - + -aq-nwb: About +aq-nwb: For Users @@ -39,7 +39,7 @@
- +
@@ -100,19 +100,21 @@
-
About
+
For Users
-

-Doxygen documentation

-

This page is auto generated using Doxygen, making use of some useful special commands.

+

This documentation is intended for users of AqNWB, e.g., developers seeking to integrate NWB with a particular data acquisition software via AqNWB.

+
diff --git a/userdocs.js b/userdocs.js new file mode 100644 index 00000000..683c756d --- /dev/null +++ b/userdocs.js @@ -0,0 +1,21 @@ +var userdocs = +[ + [ "Installing AqNWB", "install_page.html", [ + [ "Requirements", "install_page.html#user_requirements_sec", null ], + [ "Build", "install_page.html#userbuild_build_sec", null ], + [ "Install", "install_page.html#userbuild_install_sec", null ] + ] ], + [ "HDF5 I/O", "hdf5io.html", [ + [ "Chunking", "hdf5io.html#hdf5io_chunking", null ], + [ "Single-Writer Multiple-Reader (SWMR) Mode", "hdf5io.html#hdf5io_swmr", [ + [ "Why does AqNWB use SMWR mode?", "hdf5io.html#hdf5io_swmr_features", null ], + [ "Writing an NWB file with SWMR mode", "hdf5io.html#hdf5io_swmr_workflow", [ + [ "Code Examples", "hdf5io.html#hdf5io_swmr_examples", [ + [ "Workflow with SWMR", "hdf5io.html#hdf5io_swmr_examples_with_swmr", null ], + [ "Workflow with SWMR disabled", "hdf5io.html#hdf5io_noswmr_examples_without_swmr", null ] + ] ] + ] ], + [ "Reading with SWMR mode", "hdf5io.html#hdf5io_swmr_read", null ] + ] ] + ] ] +]; \ No newline at end of file diff --git a/userdocs_2install_8dox.html b/userdocs_2install_8dox.html new file mode 100644 index 00000000..a962225d --- /dev/null +++ b/userdocs_2install_8dox.html @@ -0,0 +1,116 @@ + + + + + + + + +aq-nwb: docs/pages/userdocs/install.dox File Reference + + + + + + + + + + + + + + + + + +
+
+ + + + + + + +
+
aq-nwb 0.1.0 +
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docs/pages/userdocs/install.dox File Reference
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