diff --git a/doc_build/main/user_guide/tools/manual_segmentation.md b/doc_build/main/user_guide/tools/manual_segmentation.md index b7fe006..3d0c061 100644 --- a/doc_build/main/user_guide/tools/manual_segmentation.md +++ b/doc_build/main/user_guide/tools/manual_segmentation.md @@ -36,8 +36,6 @@ Run `manual_region_seg -h` to see all options. `/home/analysis/cellfinder_output/registration/`) ##### The following options may also need to be used: -* `--save-image` Store the resulting segmented region image (e.g. for -inspecting in 2D. (default: False) * `--preview` Preview the segmented regions in brainrender (default:False) * `--debug` Debug mode. Will increase verbosity of logging and save all intermediate files for diagnosis of software issues. (default: False) @@ -51,17 +49,15 @@ take a few minutes) and then display the image in a manual_seg_window ##### To segment regions: -* Ensure that the "Regions" tab is selected (left hand side) +* Ensure that the "new_region" tab is selected (left hand side) +* Rename this region (by selecting the "new_region" text) * Navigate to where you want to draw your region of interest. * Use the scroll bar at the bottom (or left/right keys) to navigate through the image stack * Use the mouse scrollwheel to zoom in or out * Drag with the mouse the pan the view -* Select a label ID (by pressing the `+` button in the `label` row, top-left), -the ID is not important, but `0` refers to no label, so you may as well start -from 1. -* Choose a brush size (also in top left box) +* Choose a brush size (top left box) * Activate painting mode (by selecting the paintbrush, top left). You can go back to the navigation mode by selecting the magnifying glass. * Colour in your region that you want to segment, ensuring that you make a @@ -69,7 +65,16 @@ solid object. * Selecting the `ndim` toggle in the top left will extend the brush size in three dimensions (so it will colour in multiple layers). +* To add a new region press `Control+N` * Repeat above for each region you wish to segment. + * Press `Control+S` on your keyboard to save the regions. If you used the `--preview flag`, once they are saved, they will be displayed in a brainrender window. + + +##### Editing regions: +If you have already run `manual_region_seg`, and run it again, the segmented +regions will be shown. You can edit them, and press `Control+S` to resave them. +If you don't want to save any changes, press `Control+X` to exit. The regions + will still be previewed if you have selected that option. \ No newline at end of file diff --git a/docs/.buildinfo b/docs/.buildinfo index eaba643..279e694 100644 --- a/docs/.buildinfo +++ b/docs/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: ed007dbdf8172460ccc81a16ac8bf976 +config: 21f1b720085db93f2bf3fb4298a3bb15 tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/docs/_sources/main/user_guide/tools/manual_segmentation.md.txt b/docs/_sources/main/user_guide/tools/manual_segmentation.md.txt index b7fe006..3d0c061 100644 --- a/docs/_sources/main/user_guide/tools/manual_segmentation.md.txt +++ b/docs/_sources/main/user_guide/tools/manual_segmentation.md.txt @@ -36,8 +36,6 @@ Run `manual_region_seg -h` to see all options. `/home/analysis/cellfinder_output/registration/`) ##### The following options may also need to be used: -* `--save-image` Store the resulting segmented region image (e.g. for -inspecting in 2D. (default: False) * `--preview` Preview the segmented regions in brainrender (default:False) * `--debug` Debug mode. Will increase verbosity of logging and save all intermediate files for diagnosis of software issues. (default: False) @@ -51,17 +49,15 @@ take a few minutes) and then display the image in a manual_seg_window ##### To segment regions: -* Ensure that the "Regions" tab is selected (left hand side) +* Ensure that the "new_region" tab is selected (left hand side) +* Rename this region (by selecting the "new_region" text) * Navigate to where you want to draw your region of interest. * Use the scroll bar at the bottom (or left/right keys) to navigate through the image stack * Use the mouse scrollwheel to zoom in or out * Drag with the mouse the pan the view -* Select a label ID (by pressing the `+` button in the `label` row, top-left), -the ID is not important, but `0` refers to no label, so you may as well start -from 1. -* Choose a brush size (also in top left box) +* Choose a brush size (top left box) * Activate painting mode (by selecting the paintbrush, top left). You can go back to the navigation mode by selecting the magnifying glass. * Colour in your region that you want to segment, ensuring that you make a @@ -69,7 +65,16 @@ solid object. * Selecting the `ndim` toggle in the top left will extend the brush size in three dimensions (so it will colour in multiple layers). +* To add a new region press `Control+N` * Repeat above for each region you wish to segment. + * Press `Control+S` on your keyboard to save the regions. If you used the `--preview flag`, once they are saved, they will be displayed in a brainrender window. + + +##### Editing regions: +If you have already run `manual_region_seg`, and run it again, the segmented +regions will be shown. You can edit them, and press `Control+S` to resave them. +If you don't want to save any changes, press `Control+X` to exit. The regions + will still be previewed if you have selected that option. \ No newline at end of file diff --git a/docs/_static/basic.css b/docs/_static/basic.css index b04360d..0119285 100644 --- a/docs/_static/basic.css +++ b/docs/_static/basic.css @@ -4,7 +4,7 @@ * * Sphinx stylesheet -- basic theme. * - * :copyright: Copyright 2007-2019 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2020 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ diff --git a/docs/_static/doctools.js b/docs/_static/doctools.js index b33f87f..daccd20 100644 --- a/docs/_static/doctools.js +++ b/docs/_static/doctools.js @@ -4,7 +4,7 @@ * * Sphinx JavaScript utilities for all documentation. * - * :copyright: Copyright 2007-2019 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2020 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ @@ -283,10 +283,11 @@ var Documentation = { }, initOnKeyListeners: function() { - $(document).keyup(function(event) { + $(document).keydown(function(event) { var activeElementType = document.activeElement.tagName; // don't navigate when in search box or textarea - if (activeElementType !== 'TEXTAREA' && activeElementType !== 'INPUT' && activeElementType !== 'SELECT') { + if (activeElementType !== 'TEXTAREA' && activeElementType !== 'INPUT' && activeElementType !== 'SELECT' + && !event.altKey && !event.ctrlKey && !event.metaKey && !event.shiftKey) { switch (event.keyCode) { case 37: // left var prevHref = $('link[rel="prev"]').prop('href'); diff --git a/docs/_static/documentation_options.js b/docs/_static/documentation_options.js index 4790c4d..2fa8c97 100644 --- a/docs/_static/documentation_options.js +++ b/docs/_static/documentation_options.js @@ -5,6 +5,7 @@ var DOCUMENTATION_OPTIONS = { COLLAPSE_INDEX: false, BUILDER: 'html', FILE_SUFFIX: '.html', + LINK_SUFFIX: '.html', HAS_SOURCE: true, SOURCELINK_SUFFIX: '.txt', NAVIGATION_WITH_KEYS: false diff --git a/docs/_static/language_data.js b/docs/_static/language_data.js index 5266fb1..d2b4ee9 100644 --- a/docs/_static/language_data.js +++ b/docs/_static/language_data.js @@ -5,7 +5,7 @@ * This script contains the language-specific data used by searchtools.js, * namely the list of stopwords, stemmer, scorer and splitter. * - * :copyright: Copyright 2007-2019 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2020 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ diff --git a/docs/_static/searchtools.js b/docs/_static/searchtools.js index ad84587..ab56499 100644 --- a/docs/_static/searchtools.js +++ b/docs/_static/searchtools.js @@ -4,7 +4,7 @@ * * Sphinx JavaScript utilities for the full-text search. * - * :copyright: Copyright 2007-2019 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2020 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ @@ -63,6 +63,11 @@ var Search = { htmlElement.innerHTML = htmlString; $(htmlElement).find('.headerlink').remove(); docContent = $(htmlElement).find('[role=main]')[0]; + if(docContent === undefined) { + console.warn("Content block not found. Sphinx search tries to obtain it " + + "via '[role=main]'. Could you check your theme or template."); + return ""; + } return docContent.textContent || docContent.innerText; }, @@ -245,6 +250,8 @@ var Search = { if (results.length) { var item = results.pop(); var listItem = $('
  • '); + var requestUrl = ""; + var linkUrl = ""; if (DOCUMENTATION_OPTIONS.BUILDER === 'dirhtml') { // dirhtml builder var dirname = item[0] + '/'; @@ -253,15 +260,17 @@ var Search = { } else if (dirname == 'index/') { dirname = ''; } - listItem.append($('').attr('href', - DOCUMENTATION_OPTIONS.URL_ROOT + dirname + - highlightstring + item[2]).html(item[1])); + requestUrl = DOCUMENTATION_OPTIONS.URL_ROOT + dirname; + linkUrl = requestUrl; + } else { // normal html builders - listItem.append($('').attr('href', - item[0] + DOCUMENTATION_OPTIONS.FILE_SUFFIX + - highlightstring + item[2]).html(item[1])); + requestUrl = DOCUMENTATION_OPTIONS.URL_ROOT + item[0] + DOCUMENTATION_OPTIONS.FILE_SUFFIX; + linkUrl = item[0] + DOCUMENTATION_OPTIONS.LINK_SUFFIX; } + listItem.append($('').attr('href', + linkUrl + + highlightstring + item[2]).html(item[1])); if (item[3]) { listItem.append($(' (' + item[3] + ')')); Search.output.append(listItem); @@ -269,7 +278,7 @@ var Search = { displayNextItem(); }); } else if (DOCUMENTATION_OPTIONS.HAS_SOURCE) { - $.ajax({url: DOCUMENTATION_OPTIONS.URL_ROOT + item[0] + DOCUMENTATION_OPTIONS.FILE_SUFFIX, + $.ajax({url: requestUrl, dataType: "text", complete: function(jqxhr, textstatus) { var data = jqxhr.responseText; diff --git a/docs/genindex.html b/docs/genindex.html index ec8ff79..99a9189 100644 --- a/docs/genindex.html +++ b/docs/genindex.html @@ -22,10 +22,10 @@ - - - - + + + + @@ -79,15 +79,8 @@ - - - + +
    diff --git a/docs/index.html b/docs/index.html index bc7a199..6432952 100644 --- a/docs/index.html +++ b/docs/index.html @@ -21,10 +21,10 @@ - - - - + + + + @@ -35,7 +35,7 @@ - + @@ -79,15 +79,17 @@ -