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for parsing micro-manager metadata
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| <!DOCTYPE html> | |
| <head> | |
| <meta charset="utf-8"> | |
| <meta http-equiv="X-UA-Compatible" content="IE=edge,chrome=1"> | |
| <title>MM Metadata Viewer</title> | |
| <style type="text/css" media="screen"><!-- | |
| body{margin:25px;padding:0;font-family:Arial,Helvetica,sans-serif;font-size:100%} | |
| article,aside,figcaption,figure,footer,header,hgroup,nav,section{display:block} | |
| h1,h2,h3,h4{font-weight:700} | |
| h1{font-size:2em} | |
| h2{font-size:1.5em} | |
| h3{font-size:1.2em} | |
| h4{font-size:1em} | |
| a{text-decoration:underline} | |
| a:link{color:#00E} | |
| a:visited{color:#551A8B} | |
| a:active{color:#E00} | |
| a:active,a:hover{outline:0} | |
| a img{border:none} | |
| sub,sup{line-height:0} | |
| --></style> | |
| <link rel="stylesheet" href="jsontree.css"><!-- from https://github.com/jurka/jsontree --> | |
| </head> | |
| <body> | |
| <h1>Micro-Manager Metadata Viewer <sup style="color:purple"> © Liang Cai</sup></h1> | |
| <p> | |
| <span id="action_area"><input type="file" id="fileInput" /> <input type="submit" value="view" id="view" /></span> | |
| <span style="float:right;font-size:0.75em">Last updated on <script language="JavaScript" type="">document.write(document.lastModified)</script></span> | |
| </p> | |
| <div id="jsondata"><span style="color:red;background:yellow">For file size over 4M, do run it inside Chrome on a powerful computer.</span></div> | |
| </body> | |
| <script src="jquery-2.1.3.min.js"></script> | |
| <script>window.jQuery || document.write('<script src="jquery-2.1.3.min.js"><\/script>')</script> | |
| <script> | |
| var DEBUG = false, mm_file, mm_html, mm_frames, timer_start, | |
| NonShowKeys = ['UUID', | |
| 'UserName', | |
| 'Date', | |
| 'MetadataVersion', | |
| 'MicroManagerVersion', | |
| 'ROI', | |
| 'Prefix', | |
| 'Source', | |
| 'ComputerName', | |
| 'KeepShutterOpenChannels', | |
| 'KeepShutterOpenSlices', | |
| 'ChContrastMax', | |
| 'Directory', | |
| '-TransposeMirrorX', | |
| '-TransposeMirrorY', | |
| '-TransposeXY', | |
| '-Description', | |
| '-Name', | |
| '-Model', | |
| '-Mode', | |
| '-Initialize', | |
| '-FocusWheel', | |
| '-PixelType', | |
| '-AnswerTimeout', | |
| '-FanMode', | |
| '-DelayBetweenCharsMs', | |
| '-State', | |
| '-Trigger', | |
| '-Parity', | |
| '-Verbose', | |
| '-StopBits', | |
| '-BaudRate', | |
| '-Advanced | Snap Image Additional Delay (ms)', | |
| '-VerticalClockVoltage', | |
| '-SearchRange', | |
| '-TransposeCorrection', | |
| '-Camera', | |
| 'Core-SLM', | |
| '-Delay_ms', | |
| '-Handshaking', | |
| '-FarLimit', | |
| '-NearLimit', | |
| '-Region of Interest', | |
| '-OptAcquireMode', | |
| '-OptAcquireMode Description', | |
| '-1. Camera Information : | Type | Model | Serial No. |', | |
| '-2. Camera Information : | Type | Model | Serial No. |', | |
| '-DataBits', | |
| '-FocusSensitivity', | |
| '-TimeOut', | |
| 'Core-Galvo', | |
| 'Core-Focus', | |
| '-Port', | |
| '-Shutter Closing Time', | |
| '-Shutter Opening Time', | |
| 'LightPath-Label', | |
| '-KeepCleanTime', | |
| '-Shutter TTL Value', | |
| '-MaxSpeed', | |
| '-VerticalSpeed', | |
| '-CoolerMode', | |
| '-NDSetting', | |
| '-CCDTemperature', | |
| '-CCDTemperatureSetPoint', | |
| 'SimpleAutofocus-', | |
| '-ReadoutMode', | |
| '-EMSwitch', | |
| '-Busy', | |
| '-Speed', | |
| '-BaselineClamp', | |
| '-Isolated Crop Mode', | |
| 'Core-ChannelGroup', | |
| 'Core-AutoShutter', | |
| 'Core-XYStage', | |
| '-Shutter', | |
| '-TimeoutMs', | |
| '-FrameTransfer Help', | |
| '-Voltage', | |
| '-ActualInterval-ms', | |
| '-SCurve', | |
| '-StepSizeX_um', | |
| '-StepSizeY_um', | |
| '-Control', | |
| '-Controller Info', | |
| 'InitialPositionList', | |
| 'Depth', | |
| 'PixelType', | |
| 'BitDepth', | |
| 'ChContrastMin', | |
| 'Width', | |
| 'Height', | |
| 'PixelAspect', | |
| 'IJType', | |
| 'GridRow', | |
| 'Comment', | |
| 'GridColumn', | |
| 'PixelSize_um', | |
| '-ClosedPosition', | |
| '-Exposure', | |
| '-CCDTemperature Help', | |
| '-FrameTransfer', | |
| 'OlympusHub-Version', | |
| 'Core-ImageProcessor', | |
| '-Gain', | |
| '-Pre-Amp-Gain', | |
| 'CustomIntervals_ms', | |
| 'ChColors', | |
| 'SlicePosition', | |
| 'AxisPositions', | |
| '-ObjectiveTypeSetting', | |
| '-Acceleration', | |
| 'PixelSizeUm', | |
| 'Binning', | |
| '-ReadoutTime', | |
| '-Advanced | Snap Image Timing Mode', | |
| '-Binning', | |
| 'ElapsedTime-ms', | |
| 'Core-AutoFocus', | |
| '-ContinuousMode', | |
| '-Offset', | |
| 'Camera', | |
| '-AD_Converter', | |
| '-CountConvertWavelength', | |
| '-Shutter (External)', | |
| '-Shutter (Internal)', | |
| '-SpuriousNoiseFilterThreshold', | |
| 'Interval_ms', | |
| 'XPositionUm', | |
| 'YPositionUm', | |
| 'Positions', | |
| 'PositionIndex', | |
| '-CountConvert', | |
| '-SpuriousNoiseFilterDescription', | |
| '-SpuriousNoiseFilter', | |
| 'Slice', | |
| 'NextFrame', | |
| 'Frame', | |
| 'ChannelIndex', | |
| 'TransmittedLamp-Label', | |
| 'WaitInterval', | |
| '-Position', | |
| 'CameraChannelIndex', | |
| '-PiezoRange', | |
| '-PiezoPosition', | |
| '-Output_Amplifier', | |
| '-CameraName', | |
| '-TriggerMode', | |
| '-SensorTemperature', | |
| '-PixelReadoutRate', | |
| '-CameraID', | |
| '-PixelEncoding', | |
| '-Overlap', | |
| '-CurrentSoftware', | |
| '-FanSpeed', | |
| '-AccumulateCount', | |
| '-CameraModel', | |
| '-Sensitivity/DynamicRange', | |
| '-TemperatureControl', | |
| '-AuxiliaryOutSource (TTL I/O)', | |
| '-FrameRateLimits', | |
| '-SensorCooling', | |
| '-CameraFirmware', | |
| '-TemperatureStatus', | |
| '-Ext (Exp) Trigger Timeout[ms]' | |
| ], | |
| HighlightKeys = ['Slices', | |
| 'Frames', | |
| 'Channels' | |
| ]; | |
| function check_obj(obj, parent_obj, keyNameClean) { | |
| var keyNamePos = 0; | |
| if (keyNameClean.indexOf('10-3') === 0) { | |
| keyNamePos = keyNameClean.replace('10-3', '10~3').indexOf('-'); | |
| } else if (keyNameClean.indexOf('Wheel-A') === 0) { | |
| keyNamePos = keyNameClean.replace('Wheel-A', 'Wheel~A').indexOf('-'); | |
| } else { | |
| keyNamePos = keyNameClean.indexOf('-'); | |
| } | |
| if (keyNameClean === 'Slices' && typeof obj[keyNameClean] === 'number' && obj[keyNameClean] > 1) { | |
| HighlightKeys.push('z-step_um'); // only works, if Slices preceeds z-step_um | |
| HighlightKeys.push('SliceIndex'); | |
| HighlightKeys.push('ZPositionUm'); | |
| } else if (keyNameClean === 'Frames' && typeof obj[keyNameClean] === 'number' && obj[keyNameClean] > 1) { | |
| HighlightKeys.push('FrameIndex'); | |
| } else if (keyNameClean === 'Channels' && typeof obj[keyNameClean] === 'number' && obj[keyNameClean] > 1) { | |
| HighlightKeys.push('Channel'); | |
| } | |
| if ( HighlightKeys.indexOf(keyNameClean) > -1 ) { | |
| return 2; | |
| } | |
| if ( NonShowKeys.indexOf(keyNameClean) > -1 || | |
| (keyNamePos > -1 && NonShowKeys.indexOf( keyNameClean.substr(keyNamePos) ) > -1) || | |
| (keyNamePos > -1 && NonShowKeys.indexOf( keyNameClean.substr(0, keyNamePos+1) ) > -1) | |
| ) { | |
| DEBUG && console.log(keyNameClean); | |
| return 0; | |
| } | |
| if (keyNameClean.indexOf('AndorLaserCombiner-') === 0) { | |
| DEBUG && console.log(keyNameClean); | |
| return 0; | |
| } | |
| if (keyNameClean.indexOf('CSUX-') === 0) { | |
| DEBUG && console.log(keyNameClean); | |
| return 0; | |
| } | |
| if (obj[keyNameClean] === null) { | |
| DEBUG && console.log(keyNameClean); | |
| return 0; | |
| } | |
| if (keyNameClean === 'Summary') { | |
| var ele_fourUpID = parent_obj.parent().parent().parent().attr('id'); | |
| if (!ele_fourUpID) { | |
| return 0; | |
| } else if (ele_fourUpID === 'jsondata') { | |
| return 2; | |
| } | |
| } | |
| if (typeof obj[keyNameClean] === 'string' && obj[keyNameClean] === 'Default' && !parent_obj.hasClass('array')) { | |
| DEBUG && console.log(keyNameClean); | |
| return 0; | |
| } | |
| if (keyNameClean.indexOf('FrameKey-') === 0) { | |
| return 9; | |
| } | |
| return 1; | |
| } | |
| function update_timer() { | |
| setTimeout(function () { | |
| $('#text_timer').text( 'time spent: ' + Math.round(100*(performance.now()-timer_start))/100 + 'ms' ); | |
| }, 10); | |
| } | |
| function jsontree_render(obj, parent_obj) { | |
| var key, node_state, highLight, coma, aroval, | |
| ic = 0, | |
| count = 0, | |
| key_array = new Array( obj.length ); | |
| for (key in obj) { | |
| if (!key || !obj.hasOwnProperty(key)) { | |
| continue; | |
| } | |
| key_array[count] = key; | |
| count += 1; | |
| } | |
| for (ic; ic < count; ic += 1) { | |
| key = key_array[ic]; | |
| node_state = check_obj(obj, parent_obj, key); | |
| highLight = ''; | |
| coma = ''; | |
| if (ic < count-1) { | |
| coma = ','; | |
| } | |
| if (!node_state) { | |
| continue; | |
| } else if (node_state === 2) { | |
| highLight = ' style="background:cyan"'; | |
| } | |
| if (obj[key] === null) { | |
| mm_html.push('<li><span class="key"'+highLight+'>'+key+':</span><span class="null"> null </span>'+coma+'</li>'); | |
| } else if (typeof obj[key] === 'boolean') { | |
| mm_html.push('<li><span class="key"'+highLight+'>'+key+':</span><span class="boolean">'+obj[key]+'</span>'+coma+'</li>'); | |
| } else if (typeof obj[key] === 'number') { | |
| mm_html.push('<li><span class="key"'+highLight+'>'+key+':</span><span class="number">'+obj[key]+'</span>'+coma+'</li>'); | |
| } else if (typeof obj[key] === 'string') { | |
| mm_html.push('<li><span class="key"'+highLight+'>'+key+':</span><span class="string">"'+obj[key]+'"</span>'+coma+'</li>'); | |
| } else if ( $.isArray(obj[key]) ) { | |
| aroval = Math.round( 1000*performance.now() ); | |
| mm_html.push('<li><span class="key"'+highLight+'>'+key+':</span><span class="fold">[</span><ul class="array" id="ul'+aroval+'"></ul><span>]</span>'+coma+'</li>'); | |
| parent_obj.append( mm_html.join('') ); | |
| mm_html = []; | |
| jsontree_render(obj[key], $('#ul'+aroval)); | |
| } else { | |
| aroval = Math.round( 1000*performance.now() ); | |
| if (node_state === 9) { | |
| mm_frames.push(aroval); | |
| } | |
| mm_html.push('<li><span class="key"'+highLight+'>'+key+':</span><span class="fold" id="span'+aroval+'">{</span><ul class="object" id="ul'+aroval+'"></ul><span>}</span>'+coma+'</li>'); | |
| parent_obj.append( mm_html.join('') ); | |
| mm_html = []; | |
| jsontree_render(obj[key], $('#ul'+aroval)); | |
| } | |
| } | |
| if (mm_html.length > 0) { | |
| parent_obj.append( mm_html.join('') ); | |
| mm_html = []; | |
| } | |
| update_timer(); | |
| return ic; | |
| } | |
| function receivedText() { | |
| console.timeEnd('load'); | |
| update_timer(); | |
| $('#jsondata').html(''); | |
| mm_frames = []; | |
| try { | |
| console.time('parse'); | |
| var mm_json = $.parseJSON( mm_file.result ); | |
| console.timeEnd('parse'); | |
| update_timer(); | |
| console.time('paint'); | |
| // inspired by jsontree.js | |
| $('#jsondata').append('<ul class="jsontree"></ul>'); | |
| mm_html = []; | |
| jsontree_render([mm_json], $('#jsondata ul.jsontree')); | |
| console.timeEnd('paint'); | |
| update_timer(); | |
| console.time('animate'); | |
| $(document).on('click', 'ul.jsontree span.fold', function (event) { | |
| $(this).addClass('folded').next().slideUp(); | |
| event.preventDefault(); | |
| }); | |
| $(document).on('click', 'ul.jsontree span.fold.folded', function (event) { | |
| $(this).removeClass('folded').next().slideDown(); | |
| event.preventDefault(); | |
| }); | |
| var a_frame = null; | |
| while (mm_frames.length > 0) { | |
| a_frame = mm_frames.shift(); | |
| $('#span'+a_frame).addClass('folded'); | |
| $('#ul'+a_frame).css({'display': 'none'}); | |
| } | |
| console.timeEnd('animate'); | |
| update_timer(); | |
| $('#text_timer').css({'color': 'blue'}); | |
| } catch (err) { | |
| $('#jsondata').text(mm_file.result); | |
| alert(err); | |
| } | |
| return; | |
| } | |
| function upload_file(file_element) { | |
| if ( !file_element.files ) { | |
| alert('This browser does not seem to support the "files" property.'); | |
| } else if ( !file_element.files[0] ) { | |
| alert('Please select a file before clicking "view"'); | |
| } else { | |
| console.time('load'); | |
| var fi = file_element.files[0]; | |
| DEBUG && console.log(fi.name); | |
| $('#action_area').html(fi.name + '<span style="color:green;padding-left:2em;font-size:0.8em" id="text_timer">...</span>'); | |
| mm_file = new FileReader(); | |
| mm_file.onload = receivedText; | |
| mm_file.readAsText(fi); | |
| } | |
| return; | |
| } | |
| $(document).ready(function () { | |
| $('#view').on('click', function (event) { | |
| if (!window.File || !window.FileReader || !window.FileList || !window.Blob) { | |
| alert('The File APIs are not fully supported in this browser.'); | |
| return false; | |
| } | |
| timer_start = performance.now(); | |
| upload_file( document.getElementById('fileInput') ); | |
| event.preventDefault(); | |
| }); | |
| }); | |
| </script> | |
| </html> |
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