From 44438a0827803c0fd45a3f8ccc33ed0a8c87fb7a Mon Sep 17 00:00:00 2001 From: erusg Date: Thu, 16 Mar 2023 15:59:47 -0400 Subject: [PATCH 1/4] Add config params for fast segmentation of olay images --- MRISnapshot/create_report.py | 47 +++- MRISnapshot/prep_data.py | 6 +- .../AAA/QCReport/log_qc_images_all.csv | 3 + .../AAA/QCReport/log_qc_images_fail.csv | 1 + examples/scripts/AAA/QCReport/qcreport.html | 5 + .../AAA/QCReport/subjects/Scan1_mriqc.html | 117 +++++++++ .../AAA/QCReport/subjects/Scan2_mriqc.html | 117 +++++++++ .../QCReport/subjects/scripts/load_back.js | 6 + .../QCReport/subjects/scripts/misc_func.js | 30 +++ .../QCReport/subjects/scripts/pagestyle.css | 28 +++ .../QCReport/subjects/scripts/save_qcform.js | 138 +++++++++++ .../AAA/QCReport/subjects/scripts/shortcut.js | 223 ++++++++++++++++++ .../subjects/snapshots/Scan1_A_0.html | 5 + .../QCReport/subjects/snapshots/Scan1_A_0.png | Bin 0 -> 10089 bytes .../subjects/snapshots/Scan1_A_0_olay.html | 5 + 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examples/scripts/AAA/QCReport/log_qc_images_all.csv create mode 100644 examples/scripts/AAA/QCReport/log_qc_images_fail.csv create mode 100644 examples/scripts/AAA/QCReport/qcreport.html create mode 100644 examples/scripts/AAA/QCReport/subjects/Scan1_mriqc.html create mode 100644 examples/scripts/AAA/QCReport/subjects/Scan2_mriqc.html create mode 100755 examples/scripts/AAA/QCReport/subjects/scripts/load_back.js create mode 100755 examples/scripts/AAA/QCReport/subjects/scripts/misc_func.js create mode 100644 examples/scripts/AAA/QCReport/subjects/scripts/pagestyle.css create mode 100644 examples/scripts/AAA/QCReport/subjects/scripts/save_qcform.js create mode 100755 examples/scripts/AAA/QCReport/subjects/scripts/shortcut.js create mode 100644 examples/scripts/AAA/QCReport/subjects/snapshots/Scan1_A_0.html create mode 100644 examples/scripts/AAA/QCReport/subjects/snapshots/Scan1_A_0.png create mode 100644 examples/scripts/AAA/QCReport/subjects/snapshots/Scan1_A_0_olay.html create mode 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create mode 100644 examples/scripts/AAA/QCReport/subjects/snapshots/Scan2_S_4_olay.html create mode 100644 examples/scripts/AAA/QCReport/subjects/snapshots/Scan2_S_4_olay.png create mode 100644 examples/scripts/AAA/QCReport/subjects/snapshots/img_info_all.pickle create mode 100644 examples/scripts/AAA/config.csv create mode 100644 examples/scripts/AAA/list_images.csv diff --git a/MRISnapshot/create_report.py b/MRISnapshot/create_report.py index 90e32f7..e681e6d 100644 --- a/MRISnapshot/create_report.py +++ b/MRISnapshot/create_report.py @@ -52,12 +52,14 @@ def parse_config(df_conf, list_col_names): cols_default = ['id_col', 'ulay_col', 'mask_col', 'olay_col', 'olay_col2', 'sel_vals_olay', 'sel_vals_olay2', 'view_plane', 'num_slice', 'step_size_slice', 'min_vox', 'crop_to_mask', 'crop_to_olay', 'padding_ratio', 'bin_olay', + 'segment_olay', 'num_classes_olay', 'is_edge', 'alpha_olay', 'perc_high', 'perc_low', 'is_out_single', 'is_out_noqc', 'img_width', 'label_checkbox1', 'label_checkbox2', 'label_editbox'] vals_default = ['', '', '', '', '', '', '', 'A', '4', '', - '1', '0', '0', '', '1', + '1', '0', '0', '', '1', + '0', '0', '1', '1', '99', '1', '1', '0', '300', 'PASS', 'FAIL', 'Notes'] @@ -104,7 +106,8 @@ def parse_config(df_conf, list_col_names): params.sel_vals_olay2 = [int(n) for n in params.sel_vals_olay2.split('+') if n != ''] ### Convert numeric args from str to int or float - for tmp_arg in ['num_slice', 'step_size_slice', 'min_vox', 'crop_to_mask', 'crop_to_olay', 'bin_olay', + for tmp_arg in ['num_slice', 'step_size_slice', 'min_vox', 'crop_to_mask', 'crop_to_olay', 'bin_olay', + 'segment_olay', 'num_classes_olay', 'is_edge', 'is_out_single', 'is_out_noqc', 'img_width']: if params[tmp_arg] != '': params[tmp_arg] = int(params[tmp_arg]) @@ -212,6 +215,7 @@ def read_and_check_images(df_images, params, sub_index, orient = 'LPS'): qc_msg = 'Inconsistent image vs. overlay' logger.warning(' ' + qc_msg + ', subject discarded!') return qc_ok_flag, qc_msg, nii_out, fnames_out + except: nii = None qc_ok_flag = 0 @@ -322,6 +326,37 @@ def scale_img_contrast(nii_img, nii_mask, perc_low, perc_high): ']') return nii_out +def digitize_olay(nii, num_classes, perc_low = 5, perc_high = 95): + '''Simple quick segmentation of overlay image by quantizing intensities. + The purpose is to make sure that edge detection on overlay will be smooth. + Bins for digitization will be estimated from robust intensity ranges + (using percentile values to exclude outliers) + + :param nii: Input nifti image + :param num_classes: Number of classes (digits) in output image + + :return nii_out: Output nifti image + ''' + ## Check input img + if nii == None: + return nii + + ## Get img data + tmp_img = nii.get_fdata() + + ## Find min and max intensities + pmin, pmax = np.percentile(tmp_img.flatten(), [perc_low, perc_high]) + + ## Digitize image + tmp_img = np.digitize(tmp_img, np.arange(pmin, pmax, (pmax-pmin)/num_classes)) + + ## Create out nifti + nii_out = nib.Nifti1Image(tmp_img, nii.affine, nii.header) + + ## Return out nifti + logger.info(' Overlay image segmented to ' + str(num_classes) + ' classes') + return nii_out + def extract_snapshot(img_ulay, img_olay, img_olay2, params, curr_view, curr_slice, slice_index, sub_id, dir_snapshots_full, list_sel_slices): ''' Extracts an image snapshot based on input parameters, and writes it to @@ -345,7 +380,8 @@ def extract_snapshot(img_ulay, img_olay, img_olay2, params, curr_view, curr_slic img2d_ulay = img_ulay[:,:,curr_slice].astype(float) # Scale underlay image between 0 and 1 - img2d_ulay = (img2d_ulay - img2d_ulay.min()) / (img2d_ulay.max() - img2d_ulay.min()) + if img2d_ulay.max() - img2d_ulay.min() > 0: + img2d_ulay = (img2d_ulay - img2d_ulay.min()) / (img2d_ulay.max() - img2d_ulay.min()) ## Resize underlay slice #img2d_ulay = zoom(img2d_ulay, (scX,scY), order=1) @@ -633,6 +669,11 @@ def create_snapshots(params, df_images, dir_snapshots_full, out_dir): ## Scale ulay image intensities nii_ulay = scale_img_contrast(nii_ulay, nii_mask, params.perc_low, params.perc_high) + ## Digitize olay image intensities + if params.segment_olay == 1: + nii_olay = digitize_olay(nii_olay, params.num_classes_olay) + nii_olay2 = digitize_olay(nii_olay2, params.num_classes_olay) + ### Create snapshots for each orientation for view_index, curr_view in enumerate(params.view_plane): diff --git a/MRISnapshot/prep_data.py b/MRISnapshot/prep_data.py index a2a2284..a2ca74f 100644 --- a/MRISnapshot/prep_data.py +++ b/MRISnapshot/prep_data.py @@ -115,8 +115,10 @@ def prep_dataset(params): 'crop_to_mask' : 0, 'crop_to_olay' : 0, 'padding_ratio' : 0, - 'bin_olay' : 0, - 'is_edge' : 1, + 'bin_olay' : 0, + 'segment_olay' : 0, + 'num_classes_olay' : 0, + 'is_edge' : 1, 'alpha_olay' : 1, 'perc_high' : 100, 'perc_low' : 0, 'is_out_single' : 0, 'is_out_noqc' : 0, diff --git a/examples/scripts/AAA/QCReport/log_qc_images_all.csv b/examples/scripts/AAA/QCReport/log_qc_images_all.csv new file mode 100644 index 0000000..d801438 --- /dev/null +++ b/examples/scripts/AAA/QCReport/log_qc_images_all.csv @@ -0,0 +1,3 @@ +ScanID,qc_ok_flag,qc_message +Scan1,1,PASS +Scan2,1,PASS diff --git a/examples/scripts/AAA/QCReport/log_qc_images_fail.csv b/examples/scripts/AAA/QCReport/log_qc_images_fail.csv new file mode 100644 index 0000000..29956fa --- /dev/null +++ b/examples/scripts/AAA/QCReport/log_qc_images_fail.csv @@ -0,0 +1 @@ +ScanID,qc_ok_flag,qc_message diff --git a/examples/scripts/AAA/QCReport/qcreport.html b/examples/scripts/AAA/QCReport/qcreport.html new file mode 100644 index 0000000..3df7d7b --- /dev/null +++ b/examples/scripts/AAA/QCReport/qcreport.html @@ -0,0 +1,5 @@ + + + \ No newline at end of file diff --git a/examples/scripts/AAA/QCReport/subjects/Scan1_mriqc.html b/examples/scripts/AAA/QCReport/subjects/Scan1_mriqc.html new file mode 100644 index 0000000..7e18b1a --- /dev/null +++ b/examples/scripts/AAA/QCReport/subjects/Scan1_mriqc.html @@ -0,0 +1,117 @@ +
+ + +
+
+ + + + + + + + +

+

SUBJECT: 1 / 2, ID:


+

View cmd:

+fsleyes /home/guraylab/AIBIL/Github/MRISnapshot/examples/scans/Scan1/Scan1_T1.nii.gz /home/guraylab/AIBIL/Github/MRISnapshot/examples/scans/Scan1/Scan1_T1.nii.gz
+ +


+

+QC: PASS   + FAIL           +Notes           +SAVE AS:   + +
+
+
+
+

Slice: A_28

+
+ +
+
+

Slice: A_82

+
+ +
+
+

Slice: A_135

+
+ +
+
+

Slice: A_189

+
+ +
+
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Slice: A_243

+
+ +
+
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Slice: S_28

+
+ +
+
+

Slice: S_82

+
+ +
+
+

Slice: S_135

+
+ +
+
+

Slice: S_189

+
+ +
+
+

Slice: S_243

+
+ +
+
+

Slice: C_28

+
+ +
+
+

Slice: C_82

+
+ +
+
+

Slice: C_135

+
+ +
+
+

Slice: C_189

+
+ +
+
+

Slice: C_243

+
+ +
+ + +
+
+ + + diff --git a/examples/scripts/AAA/QCReport/subjects/Scan2_mriqc.html b/examples/scripts/AAA/QCReport/subjects/Scan2_mriqc.html new file mode 100644 index 0000000..575960c --- /dev/null +++ b/examples/scripts/AAA/QCReport/subjects/Scan2_mriqc.html @@ -0,0 +1,117 @@ +
+ + +
+
+ + + + + + + + +

+

SUBJECT: 2 / 2, ID:


+

View cmd:

+fsleyes /home/guraylab/AIBIL/Github/MRISnapshot/examples/scans/Scan2/Scan2_T1.nii.gz /home/guraylab/AIBIL/Github/MRISnapshot/examples/scans/Scan2/Scan2_T1.nii.gz
+ +


+

+QC: PASS   + FAIL           +Notes           +SAVE AS:   + +
+
+
+
+

Slice: A_28

+
+ +
+
+

Slice: A_82

+
+ +
+
+

Slice: A_135

+
+ +
+
+

Slice: A_189

+
+ +
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Slice: A_243

+
+ +
+
+

Slice: S_28

+
+ +
+
+

Slice: S_82

+
+ +
+
+

Slice: S_135

+
+ +
+
+

Slice: S_189

+
+ +
+
+

Slice: S_243

+
+ +
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+

Slice: C_28

+
+ +
+
+

Slice: C_82

+
+ +
+
+

Slice: C_135

+
+ +
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Slice: C_189

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+ +
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Slice: C_243

+
+ +
+ + +
+
+ + + diff --git a/examples/scripts/AAA/QCReport/subjects/scripts/load_back.js b/examples/scripts/AAA/QCReport/subjects/scripts/load_back.js new file mode 100755 index 0000000..e8d1424 --- /dev/null +++ b/examples/scripts/AAA/QCReport/subjects/scripts/load_back.js @@ -0,0 +1,6 @@ +// Set back button and page scroll position +window.onload = function () { + window.scrollBy(0,sessionStorage.getItem("page_scrollPosition")); + document.getElementById("backBut").onclick = function () { + document.location=sessionStorage.getItem("currentPage");}; +} diff --git a/examples/scripts/AAA/QCReport/subjects/scripts/misc_func.js b/examples/scripts/AAA/QCReport/subjects/scripts/misc_func.js new file mode 100755 index 0000000..6f1edb5 --- /dev/null +++ b/examples/scripts/AAA/QCReport/subjects/scripts/misc_func.js @@ -0,0 +1,30 @@ + +// Save page URL, scroll position and qc results before leaving +window.onbeforeunload = function() { + var subjidText = document.getElementById('SUBJ_ID').textContent; + sessionStorage.setItem("global_scrollPosition", window.pageYOffset); + sessionStorage.setItem("currentPage",document.URL); + saveQc(); +}; + +// window.onbeforeunload = function() { +// var subjidText = document.getElementById('SUBJ_ID'); +// sessionStorage.setItem(subjidText.textContent + "_scrollPosition", window.pageYOffset); +// sessionStorage.setItem("currentPage",document.URL); +// saveQc(); +// }; + + +// Set page scroll position and qc results +window.onload = function () { + window.scrollBy(0,sessionStorage.getItem("global_scrollPosition")); + loadQc(); +} + +// window.onload = function () { +// var subjidText = document.getElementById('SUBJ_ID'); +// window.scrollBy(0,sessionStorage.getItem(subjidText.textContent + "_scrollPosition")); +// loadQc(); +// } + + diff --git a/examples/scripts/AAA/QCReport/subjects/scripts/pagestyle.css b/examples/scripts/AAA/QCReport/subjects/scripts/pagestyle.css new file mode 100644 index 0000000..034e7cd --- /dev/null +++ b/examples/scripts/AAA/QCReport/subjects/scripts/pagestyle.css @@ -0,0 +1,28 @@ +.container{ + margin:10px; + padding:10px; +} + +.column{ + width:300px; + height:300px; + min-width:100px; + padding:5px; + margin:5px; + + background:#fff; + font-size:14px; + + display:inline-block; + position:relative; + float:center; +} + +.column img{ + width:100%; + height:100%; + margin:auto; + background:#ccc; + display:block; +} + diff --git a/examples/scripts/AAA/QCReport/subjects/scripts/save_qcform.js b/examples/scripts/AAA/QCReport/subjects/scripts/save_qcform.js new file mode 100644 index 0000000..7e7fad3 --- /dev/null +++ b/examples/scripts/AAA/QCReport/subjects/scripts/save_qcform.js @@ -0,0 +1,138 @@ +textHdr = "ID,PASS,FAIL,Notes" +// Write qc results to report +function saveQcAndReport() { + saveQc(); + saveReportToFile(); +} + +function saveSubject() { + var Check1 = document.getElementsByName('CHECK1'); + var Check2 = document.getElementsByName('CHECK2'); + var subjidText = document.getElementsByName('SUBJ_ID'); + var notesText = document.getElementsByName('TXT1'); + + textToWrite = subjidText[0].textContent; + if (Check1[i].checked) { + textToWrite = textToWrite + ',1'; + } + else { + textToWrite = textToWrite + ',0'; + } + if (Check2[0].checked) { + textToWrite = textToWrite + ',1'; + } + else { + textToWrite = textToWrite + ',0'; + } + textToWrite = textToWrite + ',' + notesText[0].value; + + var textFileAsBlob = new Blob([textToWrite], {type:'text/plain'}); + var fileNameToSaveAs = 'mriqcreport_' + subjidText[0].textContent + '.csv'; + + var downloadLink = document.createElement("a"); + downloadLink.download = fileNameToSaveAs; + downloadLink.innerHTML = "Download File"; + if (window.webkitURL != null) + { + // Chrome allows the link to be clicked + // without actually adding it to the DOM. + downloadLink.href = window.webkitURL.createObjectURL(textFileAsBlob); + } + else + { + // Firefox requires the link to be added to the DOM + // before it can be clicked. + downloadLink.href = window.URL.createObjectURL(textFileAsBlob); + downloadLink.onclick = destroyClickedElement; + downloadLink.style.display = "none"; + document.body.appendChild(downloadLink); + } + + downloadLink.click(); +} + +// Write qc results to session var +function saveQc() { + var Check1 = document.getElementsByName('CHECK1'); + var Check2 = document.getElementsByName('CHECK2'); + var subjidText = document.getElementsByName('SUBJ_ID'); + var notesText = document.getElementsByName('TXT1'); + + for (i = 0; i < subjidText.length; i++) { + textToWrite = subjidText[i].textContent; + if (Check1[i].checked) { + textToWrite = textToWrite + ',1'; + } + else { + textToWrite = textToWrite + ',0'; + } + if (Check2[i].checked) { + textToWrite = textToWrite + ',1'; + } + else { + textToWrite = textToWrite + ',0'; + } + textToWrite = textToWrite + ',' + notesText[i].value; + + sessionStorage.setItem("id_" + subjidText[i].textContent,textToWrite); + } +} + +// Load qc results from session var +function loadQc() { + var Check1 = document.getElementsByName('CHECK1'); + var Check2 = document.getElementsByName('CHECK2'); + var subjidText = document.getElementsByName('SUBJ_ID'); + var notesText = document.getElementsByName('TXT1'); + var textTmp; + var tmpArray; + + for (i = 0; i < subjidText.length; i++) { + textTmp = sessionStorage.getItem("id_" + subjidText[i].textContent) || ''; + tmpArray = textTmp.split(","); + if (tmpArray.length > 1) { + Check1[i].checked = parseInt(tmpArray[1]); + Check2[i].checked = parseInt(tmpArray[2]); + notesText[i].value = tmpArray[3]; + } + } +} + +// Write saved results to file +function saveReportToFile() { + var textToWrite = window.textHdr; + for(var i in sessionStorage) { + if (i.substr(0,3)=="id_") { + textToWrite = textToWrite + sessionStorage[i]; + } + } + + var textFileAsBlob = new Blob([textToWrite], {type:'text/plain'}); + var fileNameToSaveAs = document.getElementById("inputFileNameToSaveAs").value; + + var downloadLink = document.createElement("a"); + downloadLink.download = fileNameToSaveAs; + downloadLink.innerHTML = "Download File"; + if (window.webkitURL != null) + { + // Chrome allows the link to be clicked + // without actually adding it to the DOM. + downloadLink.href = window.webkitURL.createObjectURL(textFileAsBlob); + } + else + { + // Firefox requires the link to be added to the DOM + // before it can be clicked. + downloadLink.href = window.URL.createObjectURL(textFileAsBlob); + downloadLink.onclick = destroyClickedElement; + downloadLink.style.display = "none"; + document.body.appendChild(downloadLink); + } + + downloadLink.click(); +} + +function destroyClickedElement(event) +{ + document.body.removeChild(event.target); +} diff --git a/examples/scripts/AAA/QCReport/subjects/scripts/shortcut.js b/examples/scripts/AAA/QCReport/subjects/scripts/shortcut.js new file mode 100755 index 0000000..debaffb --- /dev/null +++ b/examples/scripts/AAA/QCReport/subjects/scripts/shortcut.js @@ -0,0 +1,223 @@ +/** + * http://www.openjs.com/scripts/events/keyboard_shortcuts/ + * Version : 2.01.B + * By Binny V A + * License : BSD + */ +shortcut = { + 'all_shortcuts':{},//All the shortcuts are stored in this array + 'add': function(shortcut_combination,callback,opt) { + //Provide a set of default options + var default_options = { + 'type':'keydown', + 'propagate':false, + 'disable_in_input':false, + 'target':document, + 'keycode':false + } + if(!opt) opt = default_options; + else { + for(var dfo in default_options) { + if(typeof opt[dfo] == 'undefined') opt[dfo] = default_options[dfo]; + } + } + + var ele = opt.target; + if(typeof opt.target == 'string') ele = document.getElementById(opt.target); + var ths = this; + shortcut_combination = shortcut_combination.toLowerCase(); + + //The function to be called at keypress + var func = function(e) { + e = e || window.event; + + if(opt['disable_in_input']) { //Don't enable shortcut keys in Input, Textarea fields + var element; + if(e.target) element=e.target; + else if(e.srcElement) element=e.srcElement; + if(element.nodeType==3) element=element.parentNode; + + if(element.tagName == 'INPUT' || element.tagName == 'TEXTAREA') return; + } + + //Find Which key is pressed + if (e.keyCode) code = e.keyCode; + else if (e.which) code = e.which; + var character = String.fromCharCode(code).toLowerCase(); + + if(code == 188) character=","; //If the user presses , when the type is onkeydown + if(code == 190) character="."; //If the user presses , when the type is onkeydown + + var keys = shortcut_combination.split("+"); + //Key Pressed - counts the number of valid keypresses - if it is same as the number of keys, the shortcut function is invoked + var kp = 0; + + //Work around for stupid Shift key bug created by using lowercase - as a result the shift+num combination was broken + var shift_nums = { + "`":"~", + "1":"!", + "2":"@", + "3":"#", + "4":"$", + "5":"%", + "6":"^", + "7":"&", + "8":"*", + "9":"(", + "0":")", + "-":"_", + "=":"+", + ";":":", + "'":"\"", + ",":"<", + ".":">", + "/":"?", + "\\":"|" + } + //Special Keys - and their codes + var special_keys = { + 'esc':27, + 'escape':27, + 'tab':9, + 'space':32, + 'return':13, + 'enter':13, + 'backspace':8, + + 'scrolllock':145, + 'scroll_lock':145, + 'scroll':145, + 'capslock':20, + 'caps_lock':20, + 'caps':20, + 'numlock':144, + 'num_lock':144, + 'num':144, + + 'pause':19, + 'break':19, + + 'insert':45, + 'home':36, + 'delete':46, + 'end':35, + + 'pageup':33, + 'page_up':33, + 'pu':33, + + 'pagedown':34, + 'page_down':34, + 'pd':34, + + 'left':37, + 'up':38, + 'right':39, + 'down':40, + + 'f1':112, + 'f2':113, + 'f3':114, + 'f4':115, + 'f5':116, + 'f6':117, + 'f7':118, + 'f8':119, + 'f9':120, + 'f10':121, + 'f11':122, + 'f12':123 + } + + var modifiers = { + shift: { wanted:false, pressed:false}, + ctrl : { wanted:false, pressed:false}, + alt : { wanted:false, pressed:false}, + meta : { wanted:false, pressed:false} //Meta is Mac specific + }; + + if(e.ctrlKey) modifiers.ctrl.pressed = true; + if(e.shiftKey) modifiers.shift.pressed = true; + if(e.altKey) modifiers.alt.pressed = true; + if(e.metaKey) modifiers.meta.pressed = true; + + for(var i=0; k=keys[i],i 1) { //If it is a special key + if(special_keys[k] == code) kp++; + + } else if(opt['keycode']) { + if(opt['keycode'] == code) kp++; + + } else { //The special keys did not match + if(character == k) kp++; + else { + if(shift_nums[character] && e.shiftKey) { //Stupid Shift key bug created by using lowercase + character = shift_nums[character]; + if(character == k) kp++; + } + } + } + } + + if(kp == keys.length && + modifiers.ctrl.pressed == modifiers.ctrl.wanted && + modifiers.shift.pressed == modifiers.shift.wanted && + modifiers.alt.pressed == modifiers.alt.wanted && + modifiers.meta.pressed == modifiers.meta.wanted) { + callback(e); + + if(!opt['propagate']) { //Stop the event + //e.cancelBubble is supported by IE - this will kill the bubbling process. + e.cancelBubble = true; + e.returnValue = false; + + //e.stopPropagation works in Firefox. + if (e.stopPropagation) { + e.stopPropagation(); + e.preventDefault(); + } + return false; + } + } + } + this.all_shortcuts[shortcut_combination] = { + 'callback':func, + 'target':ele, + 'event': opt['type'] + }; + //Attach the function with the event + if(ele.addEventListener) ele.addEventListener(opt['type'], func, false); + else if(ele.attachEvent) ele.attachEvent('on'+opt['type'], func); + else ele['on'+opt['type']] = func; + }, + + //Remove the shortcut - just specify the shortcut and I will remove the binding + 'remove':function(shortcut_combination) { + shortcut_combination = shortcut_combination.toLowerCase(); + var binding = this.all_shortcuts[shortcut_combination]; + delete(this.all_shortcuts[shortcut_combination]) + if(!binding) return; + var type = binding['event']; + var ele = binding['target']; + var callback = binding['callback']; + + if(ele.detachEvent) ele.detachEvent('on'+type, callback); + else if(ele.removeEventListener) ele.removeEventListener(type, callback, false); + else ele['on'+type] = false; + } +} \ No newline at end of file diff --git a/examples/scripts/AAA/QCReport/subjects/snapshots/Scan1_A_0.html b/examples/scripts/AAA/QCReport/subjects/snapshots/Scan1_A_0.html new file mode 100644 index 0000000..0752a3b --- /dev/null +++ b/examples/scripts/AAA/QCReport/subjects/snapshots/Scan1_A_0.html @@ -0,0 +1,5 @@ + + +
Fig: 0Slice: A_28
 +
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Fig: 0Slice: A_28
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Fig: 1Slice: A_82
+
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Fig: 1Slice: A_82
+
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Fig: 2Slice: A_135
 +
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Fig: 2Slice: A_135
 +
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Fig: 3Slice: A_189
 +
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Fig: 3Slice: A_189
 +
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Fig: 4Slice: A_243
+
+ diff --git a/examples/scripts/AAA/QCReport/subjects/snapshots/Scan1_A_4.png b/examples/scripts/AAA/QCReport/subjects/snapshots/Scan1_A_4.png new file mode 100644 index 0000000000000000000000000000000000000000..9b9c2c215a35d591688a4d12cb1e58f8a94df6b6 GIT binary patch literal 335 zcmeAS@N?(olHy`uVBq!ia0y~yVB`Z~4kn<;_se;ofE+PT7srr_Id5-o-WxTaybhloeq nLr(c^9b7qrq6j(av;G+|%-zn$+x`0CC6M8su6{1-oD!M + +
Fig: 4Slice: A_243
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+ diff --git a/examples/scripts/AAA/QCReport/subjects/snapshots/Scan1_A_4_olay.png b/examples/scripts/AAA/QCReport/subjects/snapshots/Scan1_A_4_olay.png new file mode 100644 index 0000000000000000000000000000000000000000..0e6dd509c418d26cee8563d4705dbbb346de74d9 GIT binary patch literal 833 zcmeAS@N?(olHy`uVBq!ia0y~yVB`Z~4kn<;_se;o7#Ns2JY5_^D(1YsZOC=RfQRAW zj}!m*ugSigI{Wa9*)MtYuIQ}V@{EaT<$={Z*PVYS`G6;=(M4;52dmIZ2PILDB}| + +
Fig: 10Slice: C_28
+
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Fig: 10Slice: C_28
 +
+ diff --git a/examples/scripts/AAA/QCReport/subjects/snapshots/Scan1_C_0_olay.png b/examples/scripts/AAA/QCReport/subjects/snapshots/Scan1_C_0_olay.png new file mode 100644 index 0000000000000000000000000000000000000000..cdabf2642480eb029f5b48d56e9daebbcb82ca56 GIT binary patch literal 2811 zcmd^B`#%%<8y`Z2a=IMMwUbLGxzD9+apW>_x@^gYT$(7x8V50RbmSnWn3~CIIPM&= zLmMV6nOriGSUa`i2vcOPoA2uM{eJ(4@Arq#56|;?eO}M=d7k(Cc|RGayxmlG0(Sxc z02L2+moor>%&sqIyR6i+!o@5C06RN9T%6$XMe{sX)Z~~i=>g6Jcbq!rVxG%UR5yA&p)q|_ z2{`&ozrbx@@5V=4;x(3Gq1$4Z05Y}oe(Bgd@X{I^1oD%Ubjf>9E&ir2O-+meW5fI6EQujYKw zkh*D2ef@>@Bzq(zQ55k?G(B){X-mDVFK4%=rZY3q(xZ<_DFZcPvn z-U0p7)6*3d6*1z4e&K88rO>#3i3pXkwYj#`E#R(KX`ME%>+rjUs81#SfQ^rjN8`Bs zC(G{1NlT#-_z}6K52Mx072yfTyPBGs$r-HX<~y@Z9{D*HF`Y!{rmE@Y`z*7~<*jug zGc0Jf&x`^w(sHYnb#JM%Hrg(0YiIBxK5<2O50$(n!M_!HdU~Fw%y*_Kg^C8{31}QHB%~{{v8}D2%e>+YXS|I%`=kU zwMeBVTQ>F(bteYA+0*Iz)*XNyJ|xWAhAqDdzti0np2>$J6#iU2_%6Nc0rU^{a@ph~ z+;rD2qRt7^>O6>j0QFeX>d>>FjMSIlHd+BCWNAX2H(P%PZ$S{-J#LLh7?sJbXEVU&YYVwgn&F zo+^cWccf*pZ_;A7cX2=+4)dwpca(smzxB^e$&|)|jDRH9(}HIyP>tsoEwPd2gl+9n z*1+r@!JNR{smuajf!L=qazI#4Z7w+|I^w=%7oHB<^ta&TQy3*JsyJ~a0`QH}MFmK< z&snHHV);kj6lB59i#)CJZj>H$NBXU=p*~l?E3?+;9GdK$$#Hl>B9S$@X__4AT=}L- zpXWmxhAT{mRtIcW-*+9=C60mQKNL7zzVXto(7hLjyUggFxK=y7L}Aws;xaupvqQt$ ztYq3DZt@kX(y8KDiQqKRKipL=0zXANF@0n3k=CNpb2CV<)PN5^!c!E!s$L;?!?}#F zexy(v)i3WmGxZRWn0qt4CjBMT4M(m+oy|zDWTXCqrw5}ViJlVnN z{!!DsPfMIpp_%Vsi+`%#_AYa*=1NQ3%TIe*jN^`ZaS9X8E8e0~r9EK)X-e9WDFy>w z-dBuCMI*PWdyBD+=gB2+StibFncaA+)ohEE*B&e9+VW<(z;Mo*K4_?=cGTYOqy`A62w0_Xb8=ejte zZ{SGV!z_M3O*y$YHo6b`mqESdAmm8MFD1hazt~o?ywm;ehZx)iHqw=t9ykn;`?5rQ zwg>qq{(ag&TaBh;`|GP=ms*-Ku4aSjf}Sd5UL7}6r~=*yGk$;dRj$_(tnxP7SMI`%#vcl|e{5zePL`yO)nG zjwO2Z9qp>WdU9SCE)Cse{)fTX(QQ^!w0)Q{<2bMtP&3>%NbEleh8+ZjXtL%@=P2N2 z$b2%kPEm~%alhbzH>!%R@?T}~@KJc9b~ovEoGR?~%wo776B?=%Hh4VPr5&jiXcp#1o{);uy(uf*o>^^=>_vpj8M z3)2yh*9{|Vl20!dmN9WDf3cx|O2-^~n5@k*$u%@RfZNL9Y#{b6dtp2_$F0{;G#LeV zDLU*;ZL^rsA=b6ABQG-8>xiiwi@iOKh+*-WQ7mZ01 + +
Fig: 11Slice: C_82
+
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Fig: 11Slice: C_82
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Fig: 12Slice: C_135
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Fig: 12Slice: C_135
 +
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Fig: 13Slice: C_189
 +
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Fig: 13Slice: C_189
+
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Fig: 14Slice: C_243
 +
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Fig: 14Slice: C_243
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Fig: 5Slice: S_28
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Fig: 5Slice: S_28
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Fig: 6Slice: S_82
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Fig: 6Slice: S_82
+
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Fig: 7Slice: S_135
 +
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Fig: 7Slice: S_135
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Fig: 8Slice: S_189
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Fig: 8Slice: S_189
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Fig: 9Slice: S_243
+
+ diff --git a/examples/scripts/AAA/QCReport/subjects/snapshots/Scan1_S_4.png b/examples/scripts/AAA/QCReport/subjects/snapshots/Scan1_S_4.png new file mode 100644 index 0000000000000000000000000000000000000000..8d389e047ea8e5c6e63e06a1b20034f5af1c2331 GIT binary patch literal 292 zcmeAS@N?(olHy`uVBq!ia0y~yVB`Z~4kn<;_se;ofYfVG7srr_Id2a#@&b8>7JT>5 gzopr0AQLGp8x;= literal 0 HcmV?d00001 diff --git a/examples/scripts/AAA/QCReport/subjects/snapshots/Scan1_S_4_olay.html b/examples/scripts/AAA/QCReport/subjects/snapshots/Scan1_S_4_olay.html new file mode 100644 index 0000000..84da1ea --- /dev/null +++ b/examples/scripts/AAA/QCReport/subjects/snapshots/Scan1_S_4_olay.html @@ -0,0 +1,5 @@ + + +
Fig: 9Slice: S_243
 +
+ diff --git a/examples/scripts/AAA/QCReport/subjects/snapshots/Scan1_S_4_olay.png b/examples/scripts/AAA/QCReport/subjects/snapshots/Scan1_S_4_olay.png new file mode 100644 index 0000000000000000000000000000000000000000..f5eb748f6cedd0f9e9b3603cbe680fe2e55b2105 GIT binary patch literal 801 zcmeAS@N?(olHy`uVBq!ia0y~yVB`Z~4kn<;_se;o7#Nsdc)B=-RLpsM`5^BB1%U$w zFaBA}E1TH2r1($p|E8m`f$Pt#t^02CeqdYekRx?b>N5T^Y@&OdUOxgReFjfgKbLh*2~7Z4ISOR} literal 0 HcmV?d00001 diff --git a/examples/scripts/AAA/QCReport/subjects/snapshots/Scan2_A_0.html b/examples/scripts/AAA/QCReport/subjects/snapshots/Scan2_A_0.html new file mode 100644 index 0000000..da088aa --- /dev/null +++ b/examples/scripts/AAA/QCReport/subjects/snapshots/Scan2_A_0.html @@ -0,0 +1,5 @@ + + +
Fig: 0Slice: A_28
 +
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Fig: 0Slice: A_28
+
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Fig: 1Slice: A_82
 +
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Fig: 1Slice: A_82
+
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WA?SES5qMeSiGqx(bh)Hy@c#!;P)pSS literal 0 HcmV?d00001 diff --git a/examples/scripts/AAA/QCReport/subjects/snapshots/Scan2_A_2.html b/examples/scripts/AAA/QCReport/subjects/snapshots/Scan2_A_2.html new file mode 100644 index 0000000..b2fc65c --- /dev/null +++ b/examples/scripts/AAA/QCReport/subjects/snapshots/Scan2_A_2.html @@ -0,0 +1,5 @@ + + +
Fig: 2Slice: A_135
 +
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Fig: 2Slice: A_135
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Fig: 3Slice: A_189
+
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Fig: 3Slice: A_189
+
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Fig: 4Slice: A_243
 +
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Fig: 4Slice: A_243
 +
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Fig: 10Slice: C_28
 +
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Fig: 10Slice: C_28
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Fig: 11Slice: C_82
 +
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Fig: 11Slice: C_82
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Fig: 12Slice: C_135
+
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index 0000000..afc6672 --- /dev/null +++ b/examples/scripts/AAA/QCReport/subjects/snapshots/Scan2_C_2_olay.html @@ -0,0 +1,5 @@ + + +
Fig: 12Slice: C_135
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Fig: 13Slice: C_189
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Fig: 13Slice: C_189
+
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Fig: 14Slice: C_243
+
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Fig: 14Slice: C_243
+
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Fig: 5Slice: S_28
 +
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Fig: 5Slice: S_28
 +
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Fig: 6Slice: S_82
 +
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Fig: 6Slice: S_82
+
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--git a/examples/scripts/AAA/QCReport/subjects/snapshots/Scan2_S_2.html b/examples/scripts/AAA/QCReport/subjects/snapshots/Scan2_S_2.html new file mode 100644 index 0000000..62de669 --- /dev/null +++ b/examples/scripts/AAA/QCReport/subjects/snapshots/Scan2_S_2.html @@ -0,0 +1,5 @@ + + +
Fig: 7Slice: S_135
 +
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Fig: 7Slice: S_135
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Fig: 8Slice: S_189
+
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Fig: 8Slice: S_189
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Fig: 9Slice: S_243
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Fig: 9Slice: S_243
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diff --git a/examples/scripts/AAA/list_images.csv b/examples/scripts/AAA/list_images.csv new file mode 100644 index 0000000..f5208a5 --- /dev/null +++ b/examples/scripts/AAA/list_images.csv @@ -0,0 +1,3 @@ +ScanID,UnderlayImg,OverlayImg +Scan1,/home/guraylab/AIBIL/Github/MRISnapshot/examples/scans/Scan1/Scan1_T1.nii.gz,/home/guraylab/AIBIL/Github/MRISnapshot/examples/scans/Scan1/Scan1_T1.nii.gz +Scan2,/home/guraylab/AIBIL/Github/MRISnapshot/examples/scans/Scan2/Scan2_T1.nii.gz,/home/guraylab/AIBIL/Github/MRISnapshot/examples/scans/Scan2/Scan2_T1.nii.gz From 66c920ce26d36bc4981130a968022fa656e761d7 Mon Sep 17 00:00:00 2001 From: erusg Date: Thu, 16 Mar 2023 16:00:16 -0400 Subject: [PATCH 2/4] Add config params for fast segmentation of olay images --- .../AAA/QCReport/log_qc_images_all.csv | 3 - .../AAA/QCReport/log_qc_images_fail.csv | 1 - examples/scripts/AAA/QCReport/qcreport.html | 5 - .../AAA/QCReport/subjects/Scan1_mriqc.html | 117 --------- 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index d801438..0000000 --- a/examples/scripts/AAA/QCReport/log_qc_images_all.csv +++ /dev/null @@ -1,3 +0,0 @@ -ScanID,qc_ok_flag,qc_message -Scan1,1,PASS -Scan2,1,PASS diff --git a/examples/scripts/AAA/QCReport/log_qc_images_fail.csv b/examples/scripts/AAA/QCReport/log_qc_images_fail.csv deleted file mode 100644 index 29956fa..0000000 --- a/examples/scripts/AAA/QCReport/log_qc_images_fail.csv +++ /dev/null @@ -1 +0,0 @@ -ScanID,qc_ok_flag,qc_message diff --git a/examples/scripts/AAA/QCReport/qcreport.html b/examples/scripts/AAA/QCReport/qcreport.html deleted file mode 100644 index 3df7d7b..0000000 --- a/examples/scripts/AAA/QCReport/qcreport.html +++ /dev/null @@ -1,5 +0,0 @@ - - - \ No newline at end of file diff --git a/examples/scripts/AAA/QCReport/subjects/Scan1_mriqc.html b/examples/scripts/AAA/QCReport/subjects/Scan1_mriqc.html deleted file mode 100644 index 7e18b1a..0000000 --- a/examples/scripts/AAA/QCReport/subjects/Scan1_mriqc.html +++ /dev/null @@ -1,117 +0,0 @@ -
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-fsleyes /home/guraylab/AIBIL/Github/MRISnapshot/examples/scans/Scan1/Scan1_T1.nii.gz /home/guraylab/AIBIL/Github/MRISnapshot/examples/scans/Scan1/Scan1_T1.nii.gz
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-fsleyes /home/guraylab/AIBIL/Github/MRISnapshot/examples/scans/Scan2/Scan2_T1.nii.gz /home/guraylab/AIBIL/Github/MRISnapshot/examples/scans/Scan2/Scan2_T1.nii.gz
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- - - diff --git a/examples/scripts/AAA/QCReport/subjects/scripts/load_back.js b/examples/scripts/AAA/QCReport/subjects/scripts/load_back.js deleted file mode 100755 index e8d1424..0000000 --- a/examples/scripts/AAA/QCReport/subjects/scripts/load_back.js +++ /dev/null @@ -1,6 +0,0 @@ -// Set back button and page scroll position -window.onload = function () { - window.scrollBy(0,sessionStorage.getItem("page_scrollPosition")); - document.getElementById("backBut").onclick = function () { - document.location=sessionStorage.getItem("currentPage");}; -} diff --git a/examples/scripts/AAA/QCReport/subjects/scripts/misc_func.js b/examples/scripts/AAA/QCReport/subjects/scripts/misc_func.js deleted file mode 100755 index 6f1edb5..0000000 --- a/examples/scripts/AAA/QCReport/subjects/scripts/misc_func.js +++ /dev/null @@ -1,30 +0,0 @@ - -// Save page URL, scroll position and qc results before leaving -window.onbeforeunload = function() { - var subjidText = document.getElementById('SUBJ_ID').textContent; - sessionStorage.setItem("global_scrollPosition", window.pageYOffset); - sessionStorage.setItem("currentPage",document.URL); - saveQc(); -}; - -// window.onbeforeunload = function() { -// var subjidText = document.getElementById('SUBJ_ID'); -// sessionStorage.setItem(subjidText.textContent + "_scrollPosition", window.pageYOffset); -// sessionStorage.setItem("currentPage",document.URL); -// saveQc(); -// }; - - -// Set page scroll position and qc results -window.onload = function () { - window.scrollBy(0,sessionStorage.getItem("global_scrollPosition")); - loadQc(); -} - -// window.onload = function () { -// var subjidText = document.getElementById('SUBJ_ID'); -// window.scrollBy(0,sessionStorage.getItem(subjidText.textContent + "_scrollPosition")); -// loadQc(); -// } - - diff --git a/examples/scripts/AAA/QCReport/subjects/scripts/pagestyle.css b/examples/scripts/AAA/QCReport/subjects/scripts/pagestyle.css deleted file mode 100644 index 034e7cd..0000000 --- a/examples/scripts/AAA/QCReport/subjects/scripts/pagestyle.css +++ /dev/null @@ -1,28 +0,0 @@ -.container{ - margin:10px; - padding:10px; -} - -.column{ - width:300px; - height:300px; - min-width:100px; - padding:5px; - margin:5px; - - background:#fff; - font-size:14px; - - display:inline-block; - position:relative; - float:center; -} - -.column img{ - width:100%; - height:100%; - margin:auto; - background:#ccc; - display:block; -} - diff --git a/examples/scripts/AAA/QCReport/subjects/scripts/save_qcform.js b/examples/scripts/AAA/QCReport/subjects/scripts/save_qcform.js deleted file mode 100644 index 7e7fad3..0000000 --- a/examples/scripts/AAA/QCReport/subjects/scripts/save_qcform.js +++ /dev/null @@ -1,138 +0,0 @@ -textHdr = "ID,PASS,FAIL,Notes" -// Write qc results to report -function saveQcAndReport() { - saveQc(); - saveReportToFile(); -} - -function saveSubject() { - var Check1 = document.getElementsByName('CHECK1'); - var Check2 = document.getElementsByName('CHECK2'); - var subjidText = document.getElementsByName('SUBJ_ID'); - var notesText = document.getElementsByName('TXT1'); - - textToWrite = subjidText[0].textContent; - if (Check1[i].checked) { - textToWrite = textToWrite + ',1'; - } - else { - textToWrite = textToWrite + ',0'; - } - if (Check2[0].checked) { - textToWrite = textToWrite + ',1'; - } - else { - textToWrite = textToWrite + ',0'; - } - textToWrite = textToWrite + ',' + notesText[0].value; - - var textFileAsBlob = new Blob([textToWrite], {type:'text/plain'}); - var fileNameToSaveAs = 'mriqcreport_' + subjidText[0].textContent + '.csv'; - - var downloadLink = document.createElement("a"); - downloadLink.download = fileNameToSaveAs; - downloadLink.innerHTML = "Download File"; - if (window.webkitURL != null) - { - // Chrome allows the link to be clicked - // without actually adding it to the DOM. - downloadLink.href = window.webkitURL.createObjectURL(textFileAsBlob); - } - else - { - // Firefox requires the link to be added to the DOM - // before it can be clicked. - downloadLink.href = window.URL.createObjectURL(textFileAsBlob); - downloadLink.onclick = destroyClickedElement; - downloadLink.style.display = "none"; - document.body.appendChild(downloadLink); - } - - downloadLink.click(); -} - -// Write qc results to session var -function saveQc() { - var Check1 = document.getElementsByName('CHECK1'); - var Check2 = document.getElementsByName('CHECK2'); - var subjidText = document.getElementsByName('SUBJ_ID'); - var notesText = document.getElementsByName('TXT1'); - - for (i = 0; i < subjidText.length; i++) { - textToWrite = subjidText[i].textContent; - if (Check1[i].checked) { - textToWrite = textToWrite + ',1'; - } - else { - textToWrite = textToWrite + ',0'; - } - if (Check2[i].checked) { - textToWrite = textToWrite + ',1'; - } - else { - textToWrite = textToWrite + ',0'; - } - textToWrite = textToWrite + ',' + notesText[i].value; - - sessionStorage.setItem("id_" + subjidText[i].textContent,textToWrite); - } -} - -// Load qc results from session var -function loadQc() { - var Check1 = document.getElementsByName('CHECK1'); - var Check2 = document.getElementsByName('CHECK2'); - var subjidText = document.getElementsByName('SUBJ_ID'); - var notesText = document.getElementsByName('TXT1'); - var textTmp; - var tmpArray; - - for (i = 0; i < subjidText.length; i++) { - textTmp = sessionStorage.getItem("id_" + subjidText[i].textContent) || ''; - tmpArray = textTmp.split(","); - if (tmpArray.length > 1) { - Check1[i].checked = parseInt(tmpArray[1]); - Check2[i].checked = parseInt(tmpArray[2]); - notesText[i].value = tmpArray[3]; - } - } -} - -// Write saved results to file -function saveReportToFile() { - var textToWrite = window.textHdr; - for(var i in sessionStorage) { - if (i.substr(0,3)=="id_") { - textToWrite = textToWrite + sessionStorage[i]; - } - } - - var textFileAsBlob = new Blob([textToWrite], {type:'text/plain'}); - var fileNameToSaveAs = document.getElementById("inputFileNameToSaveAs").value; - - var downloadLink = document.createElement("a"); - downloadLink.download = fileNameToSaveAs; - downloadLink.innerHTML = "Download File"; - if (window.webkitURL != null) - { - // Chrome allows the link to be clicked - // without actually adding it to the DOM. - downloadLink.href = window.webkitURL.createObjectURL(textFileAsBlob); - } - else - { - // Firefox requires the link to be added to the DOM - // before it can be clicked. - downloadLink.href = window.URL.createObjectURL(textFileAsBlob); - downloadLink.onclick = destroyClickedElement; - downloadLink.style.display = "none"; - document.body.appendChild(downloadLink); - } - - downloadLink.click(); -} - -function destroyClickedElement(event) -{ - document.body.removeChild(event.target); -} diff --git a/examples/scripts/AAA/QCReport/subjects/scripts/shortcut.js b/examples/scripts/AAA/QCReport/subjects/scripts/shortcut.js deleted file mode 100755 index debaffb..0000000 --- a/examples/scripts/AAA/QCReport/subjects/scripts/shortcut.js +++ /dev/null @@ -1,223 +0,0 @@ -/** - * http://www.openjs.com/scripts/events/keyboard_shortcuts/ - * Version : 2.01.B - * By Binny V A - * License : BSD - */ -shortcut = { - 'all_shortcuts':{},//All the shortcuts are stored in this array - 'add': function(shortcut_combination,callback,opt) { - //Provide a set of default options - var default_options = { - 'type':'keydown', - 'propagate':false, - 'disable_in_input':false, - 'target':document, - 'keycode':false - } - if(!opt) opt = default_options; - else { - for(var dfo in default_options) { - if(typeof opt[dfo] == 'undefined') opt[dfo] = default_options[dfo]; - } - } - - var ele = opt.target; - if(typeof opt.target == 'string') ele = document.getElementById(opt.target); - var ths = this; - shortcut_combination = shortcut_combination.toLowerCase(); - - //The function to be called at keypress - var func = function(e) { - e = e || window.event; - - if(opt['disable_in_input']) { //Don't enable shortcut keys in Input, Textarea fields - var element; - if(e.target) element=e.target; - else if(e.srcElement) element=e.srcElement; - if(element.nodeType==3) element=element.parentNode; - - if(element.tagName == 'INPUT' || element.tagName == 'TEXTAREA') return; - } - - //Find Which key is pressed - if (e.keyCode) code = e.keyCode; - else if (e.which) code = e.which; - var character = String.fromCharCode(code).toLowerCase(); - - if(code == 188) character=","; //If the user presses , when the type is onkeydown - if(code == 190) character="."; //If the user presses , when the type is onkeydown - - var keys = shortcut_combination.split("+"); - //Key Pressed - counts the number of valid keypresses - if it is same as the number of keys, the shortcut function is invoked - var kp = 0; - - //Work around for stupid Shift key bug created by using lowercase - as a result the shift+num combination was broken - var shift_nums = { - "`":"~", - "1":"!", - "2":"@", - "3":"#", - "4":"$", - "5":"%", - "6":"^", - "7":"&", - "8":"*", - "9":"(", - "0":")", - "-":"_", - "=":"+", - ";":":", - "'":"\"", - ",":"<", - ".":">", - "/":"?", - "\\":"|" - } - //Special Keys - and their codes - var special_keys = { - 'esc':27, - 'escape':27, - 'tab':9, - 'space':32, - 'return':13, - 'enter':13, - 'backspace':8, - - 'scrolllock':145, - 'scroll_lock':145, - 'scroll':145, - 'capslock':20, - 'caps_lock':20, - 'caps':20, - 'numlock':144, - 'num_lock':144, - 'num':144, - - 'pause':19, - 'break':19, - - 'insert':45, - 'home':36, - 'delete':46, - 'end':35, - - 'pageup':33, - 'page_up':33, - 'pu':33, - - 'pagedown':34, - 'page_down':34, - 'pd':34, - - 'left':37, - 'up':38, - 'right':39, - 'down':40, - - 'f1':112, - 'f2':113, - 'f3':114, - 'f4':115, - 'f5':116, - 'f6':117, - 'f7':118, - 'f8':119, - 'f9':120, - 'f10':121, - 'f11':122, - 'f12':123 - } - - var modifiers = { - shift: { wanted:false, pressed:false}, - ctrl : { wanted:false, pressed:false}, - alt : { wanted:false, pressed:false}, - meta : { wanted:false, pressed:false} //Meta is Mac specific - }; - - if(e.ctrlKey) modifiers.ctrl.pressed = true; - if(e.shiftKey) modifiers.shift.pressed = true; - if(e.altKey) modifiers.alt.pressed = true; - if(e.metaKey) modifiers.meta.pressed = true; - - for(var i=0; k=keys[i],i 1) { //If it is a special key - if(special_keys[k] == code) kp++; - - } else if(opt['keycode']) { - if(opt['keycode'] == code) kp++; - - } else { //The special keys did not match - if(character == k) kp++; - else { - if(shift_nums[character] && e.shiftKey) { //Stupid Shift key bug created by using lowercase - character = shift_nums[character]; - if(character == k) kp++; - } - } - } - } - - if(kp == keys.length && - modifiers.ctrl.pressed == modifiers.ctrl.wanted && - modifiers.shift.pressed == modifiers.shift.wanted && - modifiers.alt.pressed == modifiers.alt.wanted && - modifiers.meta.pressed == modifiers.meta.wanted) { - callback(e); - - if(!opt['propagate']) { //Stop the event - //e.cancelBubble is supported by IE - this will kill the bubbling process. - e.cancelBubble = true; - e.returnValue = false; - - //e.stopPropagation works in Firefox. - if (e.stopPropagation) { - e.stopPropagation(); - e.preventDefault(); - } - return false; - } - } - } - this.all_shortcuts[shortcut_combination] = { - 'callback':func, - 'target':ele, - 'event': opt['type'] - }; - //Attach the function with the event - if(ele.addEventListener) ele.addEventListener(opt['type'], func, false); - else if(ele.attachEvent) ele.attachEvent('on'+opt['type'], func); - else ele['on'+opt['type']] = func; - }, - - //Remove the shortcut - just specify the shortcut and I will remove the binding - 'remove':function(shortcut_combination) { - shortcut_combination = shortcut_combination.toLowerCase(); - var binding = this.all_shortcuts[shortcut_combination]; - delete(this.all_shortcuts[shortcut_combination]) - if(!binding) return; - var type = binding['event']; - var ele = binding['target']; - var callback = binding['callback']; - - if(ele.detachEvent) ele.detachEvent('on'+type, callback); - else if(ele.removeEventListener) ele.removeEventListener(type, callback, false); - else ele['on'+type] = false; - } -} \ No newline at end of file diff --git a/examples/scripts/AAA/QCReport/subjects/snapshots/Scan1_A_0.html b/examples/scripts/AAA/QCReport/subjects/snapshots/Scan1_A_0.html deleted file mode 100644 index 0752a3b..0000000 --- a/examples/scripts/AAA/QCReport/subjects/snapshots/Scan1_A_0.html +++ /dev/null @@ -1,5 +0,0 @@ - - -
Fig: 0Slice: A_28
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Fig: 1Slice: A_82
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Fig: 1Slice: A_82
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Fig: 2Slice: A_135
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Fig: 2Slice: A_135
 -
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Fig: 3Slice: A_189
 -
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Fig: 3Slice: A_189
 -
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Fig: 4Slice: A_243
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- diff --git a/examples/scripts/AAA/QCReport/subjects/snapshots/Scan1_A_4.png b/examples/scripts/AAA/QCReport/subjects/snapshots/Scan1_A_4.png deleted file mode 100644 index 9b9c2c215a35d591688a4d12cb1e58f8a94df6b6..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 335 zcmeAS@N?(olHy`uVBq!ia0y~yVB`Z~4kn<;_se;ofE+PT7srr_Id5-o-WxTaybhloeq nLr(c^9b7qrq6j(av;G+|%-zn$+x`0CC6M8su6{1-oD!M - -
Fig: 4Slice: A_243
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- diff --git a/examples/scripts/AAA/QCReport/subjects/snapshots/Scan1_A_4_olay.png b/examples/scripts/AAA/QCReport/subjects/snapshots/Scan1_A_4_olay.png deleted file mode 100644 index 0e6dd509c418d26cee8563d4705dbbb346de74d9..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 833 zcmeAS@N?(olHy`uVBq!ia0y~yVB`Z~4kn<;_se;o7#Ns2JY5_^D(1YsZOC=RfQRAW zj}!m*ugSigI{Wa9*)MtYuIQ}V@{EaT<$={Z*PVYS`G6;=(M4;52dmIZ2PILDB}| - -
Fig: 10Slice: C_28
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Fig: 10Slice: C_28
 -
- diff --git a/examples/scripts/AAA/QCReport/subjects/snapshots/Scan1_C_0_olay.png b/examples/scripts/AAA/QCReport/subjects/snapshots/Scan1_C_0_olay.png deleted file mode 100644 index cdabf2642480eb029f5b48d56e9daebbcb82ca56..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 2811 zcmd^B`#%%<8y`Z2a=IMMwUbLGxzD9+apW>_x@^gYT$(7x8V50RbmSnWn3~CIIPM&= zLmMV6nOriGSUa`i2vcOPoA2uM{eJ(4@Arq#56|;?eO}M=d7k(Cc|RGayxmlG0(Sxc z02L2+moor>%&sqIyR6i+!o@5C06RN9T%6$XMe{sX)Z~~i=>g6Jcbq!rVxG%UR5yA&p)q|_ z2{`&ozrbx@@5V=4;x(3Gq1$4Z05Y}oe(Bgd@X{I^1oD%Ubjf>9E&ir2O-+meW5fI6EQujYKw zkh*D2ef@>@Bzq(zQ55k?G(B){X-mDVFK4%=rZY3q(xZ<_DFZcPvn z-U0p7)6*3d6*1z4e&K88rO>#3i3pXkwYj#`E#R(KX`ME%>+rjUs81#SfQ^rjN8`Bs zC(G{1NlT#-_z}6K52Mx072yfTyPBGs$r-HX<~y@Z9{D*HF`Y!{rmE@Y`z*7~<*jug zGc0Jf&x`^w(sHYnb#JM%Hrg(0YiIBxK5<2O50$(n!M_!HdU~Fw%y*_Kg^C8{31}QHB%~{{v8}D2%e>+YXS|I%`=kU zwMeBVTQ>F(bteYA+0*Iz)*XNyJ|xWAhAqDdzti0np2>$J6#iU2_%6Nc0rU^{a@ph~ z+;rD2qRt7^>O6>j0QFeX>d>>FjMSIlHd+BCWNAX2H(P%PZ$S{-J#LLh7?sJbXEVU&YYVwgn&F zo+^cWccf*pZ_;A7cX2=+4)dwpca(smzxB^e$&|)|jDRH9(}HIyP>tsoEwPd2gl+9n z*1+r@!JNR{smuajf!L=qazI#4Z7w+|I^w=%7oHB<^ta&TQy3*JsyJ~a0`QH}MFmK< z&snHHV);kj6lB59i#)CJZj>H$NBXU=p*~l?E3?+;9GdK$$#Hl>B9S$@X__4AT=}L- zpXWmxhAT{mRtIcW-*+9=C60mQKNL7zzVXto(7hLjyUggFxK=y7L}Aws;xaupvqQt$ ztYq3DZt@kX(y8KDiQqKRKipL=0zXANF@0n3k=CNpb2CV<)PN5^!c!E!s$L;?!?}#F zexy(v)i3WmGxZRWn0qt4CjBMT4M(m+oy|zDWTXCqrw5}ViJlVnN z{!!DsPfMIpp_%Vsi+`%#_AYa*=1NQ3%TIe*jN^`ZaS9X8E8e0~r9EK)X-e9WDFy>w z-dBuCMI*PWdyBD+=gB2+StibFncaA+)ohEE*B&e9+VW<(z;Mo*K4_?=cGTYOqy`A62w0_Xb8=ejte zZ{SGV!z_M3O*y$YHo6b`mqESdAmm8MFD1hazt~o?ywm;ehZx)iHqw=t9ykn;`?5rQ zwg>qq{(ag&TaBh;`|GP=ms*-Ku4aSjf}Sd5UL7}6r~=*yGk$;dRj$_(tnxP7SMI`%#vcl|e{5zePL`yO)nG zjwO2Z9qp>WdU9SCE)Cse{)fTX(QQ^!w0)Q{<2bMtP&3>%NbEleh8+ZjXtL%@=P2N2 z$b2%kPEm~%alhbzH>!%R@?T}~@KJc9b~ovEoGR?~%wo776B?=%Hh4VPr5&jiXcp#1o{);uy(uf*o>^^=>_vpj8M z3)2yh*9{|Vl20!dmN9WDf3cx|O2-^~n5@k*$u%@RfZNL9Y#{b6dtp2_$F0{;G#LeV zDLU*;ZL^rsA=b6ABQG-8>xiiwi@iOKh+*-WQ7mZ01 - -
Fig: 11Slice: C_82
-
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Fig: 11Slice: C_82
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Fig: 12Slice: C_135
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Fig: 12Slice: C_135
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Fig: 13Slice: C_189
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Fig: 13Slice: C_189
-
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Fig: 14Slice: C_243
 -
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Fig: 14Slice: C_243
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Fig: 5Slice: S_28
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- diff --git a/examples/scripts/AAA/QCReport/subjects/snapshots/Scan1_S_0.png b/examples/scripts/AAA/QCReport/subjects/snapshots/Scan1_S_0.png deleted file mode 100644 index 8d389e047ea8e5c6e63e06a1b20034f5af1c2331..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 292 zcmeAS@N?(olHy`uVBq!ia0y~yVB`Z~4kn<;_se;ofYfVG7srr_Id2a#@&b8>7JT>5 gzopr0AQLGp8x;= diff --git a/examples/scripts/AAA/QCReport/subjects/snapshots/Scan1_S_0_olay.html b/examples/scripts/AAA/QCReport/subjects/snapshots/Scan1_S_0_olay.html deleted file mode 100644 index d5dbfc4..0000000 --- a/examples/scripts/AAA/QCReport/subjects/snapshots/Scan1_S_0_olay.html +++ /dev/null @@ -1,5 +0,0 @@ - - -
Fig: 5Slice: S_28
 -
- diff --git a/examples/scripts/AAA/QCReport/subjects/snapshots/Scan1_S_0_olay.png b/examples/scripts/AAA/QCReport/subjects/snapshots/Scan1_S_0_olay.png deleted file mode 100644 index f5eb748f6cedd0f9e9b3603cbe680fe2e55b2105..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 801 zcmeAS@N?(olHy`uVBq!ia0y~yVB`Z~4kn<;_se;o7#Nsdc)B=-RLpsM`5^BB1%U$w zFaBA}E1TH2r1($p|E8m`f$Pt#t^02CeqdYekRx?b>N5T^Y@&OdUOxgReFjfgKbLh*2~7Z4ISOR} diff --git a/examples/scripts/AAA/QCReport/subjects/snapshots/Scan1_S_1.html b/examples/scripts/AAA/QCReport/subjects/snapshots/Scan1_S_1.html deleted file mode 100644 index 029d4aa..0000000 --- a/examples/scripts/AAA/QCReport/subjects/snapshots/Scan1_S_1.html +++ /dev/null @@ -1,5 +0,0 @@ - - -
Fig: 6Slice: S_82
 -
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Fig: 6Slice: S_82
-
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Fig: 7Slice: S_135
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Fig: 7Slice: S_135
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Fig: 8Slice: S_189
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Fig: 8Slice: S_189
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Fig: 9Slice: S_243
-
- diff --git a/examples/scripts/AAA/QCReport/subjects/snapshots/Scan1_S_4.png b/examples/scripts/AAA/QCReport/subjects/snapshots/Scan1_S_4.png deleted file mode 100644 index 8d389e047ea8e5c6e63e06a1b20034f5af1c2331..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 292 zcmeAS@N?(olHy`uVBq!ia0y~yVB`Z~4kn<;_se;ofYfVG7srr_Id2a#@&b8>7JT>5 gzopr0AQLGp8x;= diff --git a/examples/scripts/AAA/QCReport/subjects/snapshots/Scan1_S_4_olay.html b/examples/scripts/AAA/QCReport/subjects/snapshots/Scan1_S_4_olay.html deleted file mode 100644 index 84da1ea..0000000 --- a/examples/scripts/AAA/QCReport/subjects/snapshots/Scan1_S_4_olay.html +++ /dev/null @@ -1,5 +0,0 @@ - - -
Fig: 9Slice: S_243
 -
- diff --git a/examples/scripts/AAA/QCReport/subjects/snapshots/Scan1_S_4_olay.png b/examples/scripts/AAA/QCReport/subjects/snapshots/Scan1_S_4_olay.png deleted file mode 100644 index f5eb748f6cedd0f9e9b3603cbe680fe2e55b2105..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 801 zcmeAS@N?(olHy`uVBq!ia0y~yVB`Z~4kn<;_se;o7#Nsdc)B=-RLpsM`5^BB1%U$w zFaBA}E1TH2r1($p|E8m`f$Pt#t^02CeqdYekRx?b>N5T^Y@&OdUOxgReFjfgKbLh*2~7Z4ISOR} diff --git a/examples/scripts/AAA/QCReport/subjects/snapshots/Scan2_A_0.html b/examples/scripts/AAA/QCReport/subjects/snapshots/Scan2_A_0.html deleted file mode 100644 index da088aa..0000000 --- a/examples/scripts/AAA/QCReport/subjects/snapshots/Scan2_A_0.html +++ /dev/null @@ -1,5 +0,0 @@ - - -
Fig: 0Slice: A_28
 -
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Fig: 0Slice: A_28
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Fig: 1Slice: A_82
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Fig: 1Slice: A_82
-
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WA?SES5qMeSiGqx(bh)Hy@c#!;P)pSS diff --git a/examples/scripts/AAA/QCReport/subjects/snapshots/Scan2_A_2.html b/examples/scripts/AAA/QCReport/subjects/snapshots/Scan2_A_2.html deleted file mode 100644 index b2fc65c..0000000 --- a/examples/scripts/AAA/QCReport/subjects/snapshots/Scan2_A_2.html +++ /dev/null @@ -1,5 +0,0 @@ - - -
Fig: 2Slice: A_135
 -
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Fig: 2Slice: A_135
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Fig: 3Slice: A_189
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Fig: 3Slice: A_189
-
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Fig: 4Slice: A_243
 -
- diff --git a/examples/scripts/AAA/QCReport/subjects/snapshots/Scan2_A_4.png b/examples/scripts/AAA/QCReport/subjects/snapshots/Scan2_A_4.png deleted file mode 100644 index 8b5db5db96d372c665da2821adff2b43c07a4ecb..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 468 zcmeAS@N?(olHy`uVBq!ia0y~yVB`Z~4kn<;_se;ofSlQ$E{-7;bKc%{B~udc zgG&fou?0}cgZep+>p!ph7-+-T3>H@SG;eQ1R*m)=t=(KMF04vi8(xcq_a}uzG$|~) zH7~z@--Ra{|r!PeE2tq9T8Z-aqU&S|C qM`ub%yMleQ*0lLIOauA!0Ui0pTXfBD9;sakGQ`u>&t;ucLK6U1hkA7Y diff --git a/examples/scripts/AAA/QCReport/subjects/snapshots/Scan2_A_4_olay.html b/examples/scripts/AAA/QCReport/subjects/snapshots/Scan2_A_4_olay.html deleted file mode 100644 index 477a873..0000000 --- a/examples/scripts/AAA/QCReport/subjects/snapshots/Scan2_A_4_olay.html +++ /dev/null @@ -1,5 +0,0 @@ - - -
Fig: 4Slice: A_243
 -
- diff --git a/examples/scripts/AAA/QCReport/subjects/snapshots/Scan2_A_4_olay.png b/examples/scripts/AAA/QCReport/subjects/snapshots/Scan2_A_4_olay.png deleted file mode 100644 index 18cb07dd6ecf99a0f2b266af9efe6d4065f46089..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 921 zcmeAS@N?(olHy`uVBq!ia0y~yVB`Z~4kn<;_se;o7#NrnJY5_^D(1YsYnXRffx#hg z_p86_eYR`7dUXGaAYWbnsR;*9iwij4IL^ir)aaaidtaJ8a}C={2PILDB}|$lW67dBYVHrf2f)H z_nF=A*@mki;oMvO`r(A?*9%cBO-erfbKdv;H~wtmS$yhb-CN;gNk~jQO%YQ+ZM3<~ z`CEgdDma?LC#?Ux>SI_BG@6pu78(5)-KMn|(=R=R{N7(sQ3RAB&JW*^s9DlJ+*YE>|w>zRV#2s|K_jnpPrAJo(MHiDE;;I=WqV~ zzuB_i?)lgA&~zjA{K3D>Gbs-zq}qlI$Mgft5pR;e2_JC(!I+R~D&iMnF9XbS44$rj JF6*2UngB^!LPr1q diff --git a/examples/scripts/AAA/QCReport/subjects/snapshots/Scan2_C_0.html b/examples/scripts/AAA/QCReport/subjects/snapshots/Scan2_C_0.html deleted file mode 100644 index e154af9..0000000 --- a/examples/scripts/AAA/QCReport/subjects/snapshots/Scan2_C_0.html +++ /dev/null @@ -1,5 +0,0 @@ - - -
Fig: 10Slice: C_28
 -
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Fig: 10Slice: C_28
 -
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Fig: 11Slice: C_82
 -
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diff --git a/examples/scripts/AAA/QCReport/subjects/snapshots/Scan2_C_1_olay.html b/examples/scripts/AAA/QCReport/subjects/snapshots/Scan2_C_1_olay.html deleted file mode 100644 index 7e01413..0000000 --- a/examples/scripts/AAA/QCReport/subjects/snapshots/Scan2_C_1_olay.html +++ /dev/null @@ -1,5 +0,0 @@ - - -
Fig: 11Slice: C_82
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Fig: 12Slice: C_135
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Fig: 12Slice: C_135
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Fig: 13Slice: C_189
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Fig: 13Slice: C_189
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Fig: 14Slice: C_243
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Fig: 14Slice: C_243
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Fig: 5Slice: S_28
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- diff --git a/examples/scripts/AAA/QCReport/subjects/snapshots/Scan2_S_0.png b/examples/scripts/AAA/QCReport/subjects/snapshots/Scan2_S_0.png deleted file mode 100644 index 8d389e047ea8e5c6e63e06a1b20034f5af1c2331..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 292 zcmeAS@N?(olHy`uVBq!ia0y~yVB`Z~4kn<;_se;ofYfVG7srr_Id2a#@&b8>7JT>5 gzopr0AQLGp8x;= diff --git a/examples/scripts/AAA/QCReport/subjects/snapshots/Scan2_S_0_olay.html b/examples/scripts/AAA/QCReport/subjects/snapshots/Scan2_S_0_olay.html deleted file mode 100644 index 5f9e1ff..0000000 --- a/examples/scripts/AAA/QCReport/subjects/snapshots/Scan2_S_0_olay.html +++ /dev/null @@ -1,5 +0,0 @@ - - -
Fig: 5Slice: S_28
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- diff --git a/examples/scripts/AAA/QCReport/subjects/snapshots/Scan2_S_0_olay.png b/examples/scripts/AAA/QCReport/subjects/snapshots/Scan2_S_0_olay.png deleted file mode 100644 index f5eb748f6cedd0f9e9b3603cbe680fe2e55b2105..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 801 zcmeAS@N?(olHy`uVBq!ia0y~yVB`Z~4kn<;_se;o7#Nsdc)B=-RLpsM`5^BB1%U$w zFaBA}E1TH2r1($p|E8m`f$Pt#t^02CeqdYekRx?b>N5T^Y@&OdUOxgReFjfgKbLh*2~7Z4ISOR} diff --git a/examples/scripts/AAA/QCReport/subjects/snapshots/Scan2_S_1.html b/examples/scripts/AAA/QCReport/subjects/snapshots/Scan2_S_1.html deleted file mode 100644 index e2b2abb..0000000 --- a/examples/scripts/AAA/QCReport/subjects/snapshots/Scan2_S_1.html +++ /dev/null @@ -1,5 +0,0 @@ - - -
Fig: 6Slice: S_82
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Fig: 6Slice: S_82
-
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a/examples/scripts/AAA/QCReport/subjects/snapshots/Scan2_S_2.html b/examples/scripts/AAA/QCReport/subjects/snapshots/Scan2_S_2.html deleted file mode 100644 index 62de669..0000000 --- a/examples/scripts/AAA/QCReport/subjects/snapshots/Scan2_S_2.html +++ /dev/null @@ -1,5 +0,0 @@ - - -
Fig: 7Slice: S_135
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Fig: 7Slice: S_135
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Fig: 8Slice: S_189
-
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Fig: 8Slice: S_189
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Fig: 9Slice: S_243
 -
- diff --git a/examples/scripts/AAA/QCReport/subjects/snapshots/Scan2_S_4.png b/examples/scripts/AAA/QCReport/subjects/snapshots/Scan2_S_4.png deleted file mode 100644 index 8d389e047ea8e5c6e63e06a1b20034f5af1c2331..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 292 zcmeAS@N?(olHy`uVBq!ia0y~yVB`Z~4kn<;_se;ofYfVG7srr_Id2a#@&b8>7JT>5 gzopr0AQLGp8x;= diff --git a/examples/scripts/AAA/QCReport/subjects/snapshots/Scan2_S_4_olay.html b/examples/scripts/AAA/QCReport/subjects/snapshots/Scan2_S_4_olay.html deleted file mode 100644 index d1cf69a..0000000 --- a/examples/scripts/AAA/QCReport/subjects/snapshots/Scan2_S_4_olay.html +++ /dev/null @@ -1,5 +0,0 @@ - - -
Fig: 9Slice: S_243
 -
- diff --git a/examples/scripts/AAA/QCReport/subjects/snapshots/Scan2_S_4_olay.png b/examples/scripts/AAA/QCReport/subjects/snapshots/Scan2_S_4_olay.png deleted file mode 100644 index f5eb748f6cedd0f9e9b3603cbe680fe2e55b2105..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 801 zcmeAS@N?(olHy`uVBq!ia0y~yVB`Z~4kn<;_se;o7#Nsdc)B=-RLpsM`5^BB1%U$w zFaBA}E1TH2r1($p|E8m`f$Pt#t^02CeqdYekRx?b>N5T^Y@&OdUOxgReFjfgKbLh*2~7Z4ISOR} diff --git a/examples/scripts/AAA/QCReport/subjects/snapshots/img_info_all.pickle b/examples/scripts/AAA/QCReport/subjects/snapshots/img_info_all.pickle deleted file mode 100644 index b8542c778233106cd680dd0c8a770aa8b9c8d791..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 1887 zcmds1L2uJA6mB+3)wKr@n-Jmxx1JiB4XL1AN)D)WRASi`S#E0PNNEzq39OTlxD1%& z+aCXhU&SAQXQzq1GeaOECH`LG@3WutzW3?Yx06mwUvFXX5eBj=$_0s%B|C#zOWxMe z5@b6FX)*%2^Ddz)M#`A3K_0n0T`~8x%;`F&3wJVoF+Fl$Mg=by?(5@ekkCxjduDcw0qUQm9_`6g^Rt9*awouG+}_LOJ@So3GnuT z$$N1m3L;ocL>z@o5E{pN)?QMsvh^@bb2eO+aS_oRa|hWcISbQ76nPmIaE0fkCxYxG z%WBFM9_I!4&H}!`F$`wTtbGA|PqvrEI%A5m6^-HYYxQ+oI)^Zy&tLt-OFw3<0v4D4 z;9>Q*T5mSv=gs(iGyd3&fYbRdzpqy159~D`{}mM`?}|-15M4s`k#==8kO_GLvcXts z4aWb~;C%}pG&r!h0WsWw7;ZoeHz0=VTU_7b`WDx>xIS{3+--6RX;wsO(o{$C)b+6Nvn9#YtFjfd2G!!;iAi1CoZhHE^e-W#s=5ck#2>ni^r I?ZSq?0ItqXxc~qF diff --git a/examples/scripts/AAA/config.csv b/examples/scripts/AAA/config.csv deleted file mode 100644 index 412b1d6..0000000 --- a/examples/scripts/AAA/config.csv +++ /dev/null @@ -1,28 +0,0 @@ -ParamName,ParamValue -id_col,ScanID -ulay_col,UnderlayImg -mask_col, -olay_col,OverlayImg -olay_col2, -sel_vals_olay, -sel_vals_olay2, -view_plane,A+S+C -num_slice,5 -step_size_slice, -min_vox,1 -crop_to_mask,0 -crop_to_olay,0 -padding_ratio,0 -bin_olay,0 -segment_olay,1 -num_classes_olay,2 -is_edge,1 -alpha_olay,1 -perc_high,100 -perc_low,0 -is_out_single,0 -is_out_noqc,0 -img_width,300 -label_checkbox1,PASS -label_checkbox2,FAIL -label_editbox,Notes diff --git a/examples/scripts/AAA/list_images.csv b/examples/scripts/AAA/list_images.csv deleted file mode 100644 index f5208a5..0000000 --- a/examples/scripts/AAA/list_images.csv +++ /dev/null @@ -1,3 +0,0 @@ -ScanID,UnderlayImg,OverlayImg -Scan1,/home/guraylab/AIBIL/Github/MRISnapshot/examples/scans/Scan1/Scan1_T1.nii.gz,/home/guraylab/AIBIL/Github/MRISnapshot/examples/scans/Scan1/Scan1_T1.nii.gz -Scan2,/home/guraylab/AIBIL/Github/MRISnapshot/examples/scans/Scan2/Scan2_T1.nii.gz,/home/guraylab/AIBIL/Github/MRISnapshot/examples/scans/Scan2/Scan2_T1.nii.gz From 122eff6fd1819cb47e3d747943791ea497c14bc5 Mon Sep 17 00:00:00 2001 From: erusg Date: Thu, 16 Mar 2023 16:29:10 -0400 Subject: [PATCH 3/4] Add config params for fast segmentation of olay images --- MRISnapshot/create_report.py | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/MRISnapshot/create_report.py b/MRISnapshot/create_report.py index e681e6d..95710fa 100644 --- a/MRISnapshot/create_report.py +++ b/MRISnapshot/create_report.py @@ -121,6 +121,20 @@ def parse_config(df_conf, list_col_names): params.alpha_olay = 1 logger.warning(' Parameter alpha_olay is set to 1, because is_edge was set to 1') + ### Correct inconsistent parameters + if (params.segment_olay == 1): + if params.num_classes_olay > 10: + params.num_classes_olay = 10 + logger.warning(' Parameter num_classes_olay is set to 10 (max value)') + if params.num_classes_olay < 2: + params.num_classes_olay = 2 + logger.warning(' Parameter num_classes_olay is set to 2 (min value)') + if params.is_edge == 0: + params.is_edge = 1 + logger.warning(' Parameter is_edge is set to 1, because segment_olay was set to 1') + params.alpha_olay = 1 + logger.warning(' Parameter alpha_olay is set to 1, because is_edge was set to 1') + return params def create_dir(dir_name): From a9a8e4d513668df368c9b2e45c1f076c88525da0 Mon Sep 17 00:00:00 2001 From: erusg Date: Wed, 7 Feb 2024 12:45:23 -0500 Subject: [PATCH 4/4] Fix bug: comparison of affine matrices for overlay and underlay was too sensitive; updated with a more tolerant comparison --- MRISnapshot/create_report.py | 20 ++++++++++++++++---- 1 file changed, 16 insertions(+), 4 deletions(-) diff --git a/MRISnapshot/create_report.py b/MRISnapshot/create_report.py index 95710fa..310fb98 100644 --- a/MRISnapshot/create_report.py +++ b/MRISnapshot/create_report.py @@ -216,6 +216,14 @@ def read_and_check_images(df_images, params, sub_index, orient = 'LPS'): else: try: nii = nib.load(fname) + except: + nii = None + qc_ok_flag = 0 + qc_msg = 'Could not read ' + col_name + ' image ' + fname + logger.warning(' ' + qc_msg + ', subject discarded!') + return qc_ok_flag, qc_msg, nii_out, fnames_out + + try: orig_ornt = nib.io_orientation(nii.affine) targ_ornt = axcodes2ornt(orient) if np.all(orig_ornt == targ_ornt) == False: @@ -224,18 +232,22 @@ def read_and_check_images(df_images, params, sub_index, orient = 'LPS'): if ref_affine == []: ref_affine = nii.affine else: - if (ref_affine - nii.affine).sum() != 0: + + ## We compare the affine matrix for underlay and overlay images + ## - we use 3 digit precision + ## otherwise it may be too sensitive to numeric differences in headers + if (np.abs(ref_affine - nii.affine).sum()) > 0.001: qc_ok_flag = 0 - qc_msg = 'Inconsistent image vs. overlay' + qc_msg = 'Inconsistent image vs. overlay: affine matrices in headers not consistent' logger.warning(' ' + qc_msg + ', subject discarded!') return qc_ok_flag, qc_msg, nii_out, fnames_out - except: nii = None qc_ok_flag = 0 - qc_msg = 'Could not read ' + col_name + ' image ' + fname + qc_msg = 'Could not reorient ' + col_name + ' image ' + fname logger.warning(' ' + qc_msg + ', subject discarded!') return qc_ok_flag, qc_msg, nii_out, fnames_out + nii_out.append(nii) fnames_out.append(fname)