diff --git a/check_th_all_ch_per_image.ipynb b/check_th_all_ch_per_image.ipynb
index 23880b1..ae68821 100644
--- a/check_th_all_ch_per_image.ipynb
+++ b/check_th_all_ch_per_image.ipynb
@@ -2,7 +2,7 @@
"cells": [
{
"cell_type": "code",
- "execution_count": 1,
+ "execution_count": 6,
"metadata": {},
"outputs": [
{
@@ -27,13 +27,11 @@
" }\n",
"\n",
" var force = true;\n",
+ " var py_version = '3.4.1'.replace('rc', '-rc.').replace('.dev', '-dev.');\n",
+ " var reloading = false;\n",
+ " var Bokeh = root.Bokeh;\n",
"\n",
- " if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n",
- " root._bokeh_onload_callbacks = [];\n",
- " root._bokeh_is_loading = undefined;\n",
- " }\n",
- "\n",
- " if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n",
+ " if (typeof (root._bokeh_timeout) === \"undefined\" || force) {\n",
" root._bokeh_timeout = Date.now() + 5000;\n",
" root._bokeh_failed_load = false;\n",
" }\n",
@@ -45,26 +43,30 @@
" callback();\n",
" });\n",
" } finally {\n",
- " delete root._bokeh_onload_callbacks\n",
+ " delete root._bokeh_onload_callbacks;\n",
" }\n",
" console.debug(\"Bokeh: all callbacks have finished\");\n",
" }\n",
"\n",
- " function load_libs(css_urls, js_urls, js_modules, callback) {\n",
+ " function load_libs(css_urls, js_urls, js_modules, js_exports, callback) {\n",
" if (css_urls == null) css_urls = [];\n",
" if (js_urls == null) js_urls = [];\n",
" if (js_modules == null) js_modules = [];\n",
+ " if (js_exports == null) js_exports = {};\n",
"\n",
" root._bokeh_onload_callbacks.push(callback);\n",
+ "\n",
" if (root._bokeh_is_loading > 0) {\n",
" console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n",
" return null;\n",
" }\n",
- " if (js_urls.length === 0 && js_modules.length === 0) {\n",
+ " if (js_urls.length === 0 && js_modules.length === 0 && Object.keys(js_exports).length === 0) {\n",
" run_callbacks();\n",
" return null;\n",
" }\n",
- " console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n",
+ " if (!reloading) {\n",
+ " console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n",
+ " }\n",
"\n",
" function on_load() {\n",
" root._bokeh_is_loading--;\n",
@@ -73,26 +75,15 @@
" run_callbacks()\n",
" }\n",
" }\n",
+ " window._bokeh_on_load = on_load\n",
"\n",
" function on_error() {\n",
" console.error(\"failed to load \" + url);\n",
" }\n",
"\n",
- " for (var i = 0; i < css_urls.length; i++) {\n",
- " var url = css_urls[i];\n",
- " const element = document.createElement(\"link\");\n",
- " element.onload = on_load;\n",
- " element.onerror = on_error;\n",
- " element.rel = \"stylesheet\";\n",
- " element.type = \"text/css\";\n",
- " element.href = url;\n",
- " console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n",
- " document.body.appendChild(element);\n",
- " }\n",
- "\n",
" var skip = [];\n",
" if (window.requirejs) {\n",
- " window.requirejs.config({'packages': {}, 'paths': {'tabulator': 'https://cdn.jsdelivr.net/npm/tabulator-tables@5.3.2/dist/js/tabulator', 'moment': 'https://cdn.jsdelivr.net/npm/luxon/build/global/luxon.min', 'gridstack': 'https://cdn.jsdelivr.net/npm/gridstack@4.2.5/dist/gridstack-h5', 'notyf': 'https://cdn.jsdelivr.net/npm/notyf@3/notyf.min'}, 'shim': {'gridstack': {'exports': 'GridStack'}}});\n",
+ " window.requirejs.config({'packages': {}, 'paths': {'tabulator': 'https://cdn.jsdelivr.net/npm/tabulator-tables@5.5.0/dist/js/tabulator.min', 'moment': 'https://cdn.jsdelivr.net/npm/luxon/build/global/luxon.min'}, 'shim': {}});\n",
" require([\"tabulator\"], function(Tabulator) {\n",
"\twindow.Tabulator = Tabulator\n",
"\ton_load()\n",
@@ -101,39 +92,54 @@
"\twindow.moment = moment\n",
"\ton_load()\n",
" })\n",
- " require([\"gridstack\"], function(GridStack) {\n",
- "\twindow.GridStack = GridStack\n",
- "\ton_load()\n",
- " })\n",
- " require([\"notyf\"], function() {\n",
- "\ton_load()\n",
- " })\n",
- " root._bokeh_is_loading = css_urls.length + 4;\n",
+ " root._bokeh_is_loading = css_urls.length + 2;\n",
" } else {\n",
- " root._bokeh_is_loading = css_urls.length + js_urls.length + js_modules.length;\n",
- " } if (((window['Tabulator'] !== undefined) && (!(window['Tabulator'] instanceof HTMLElement))) || window.requirejs) {\n",
- " var urls = ['https://cdn.holoviz.org/panel/0.14.3/dist/bundled/datatabulator/tabulator-tables@5.3.2/dist/js/tabulator.js'];\n",
- " for (var i = 0; i < urls.length; i++) {\n",
- " skip.push(urls[i])\n",
+ " root._bokeh_is_loading = css_urls.length + js_urls.length + js_modules.length + Object.keys(js_exports).length;\n",
+ " }\n",
+ "\n",
+ " var existing_stylesheets = []\n",
+ " var links = document.getElementsByTagName('link')\n",
+ " for (var i = 0; i < links.length; i++) {\n",
+ " var link = links[i]\n",
+ " if (link.href != null) {\n",
+ "\texisting_stylesheets.push(link.href)\n",
" }\n",
- " } if (((window['moment'] !== undefined) && (!(window['moment'] instanceof HTMLElement))) || window.requirejs) {\n",
- " var urls = ['https://cdn.holoviz.org/panel/0.14.3/dist/bundled/datatabulator/luxon/build/global/luxon.min.js'];\n",
- " for (var i = 0; i < urls.length; i++) {\n",
- " skip.push(urls[i])\n",
+ " }\n",
+ " for (var i = 0; i < css_urls.length; i++) {\n",
+ " var url = css_urls[i];\n",
+ " if (existing_stylesheets.indexOf(url) !== -1) {\n",
+ "\ton_load()\n",
+ "\tcontinue;\n",
" }\n",
- " } if (((window['GridStack'] !== undefined) && (!(window['GridStack'] instanceof HTMLElement))) || window.requirejs) {\n",
- " var urls = ['https://cdn.holoviz.org/panel/0.14.3/dist/bundled/gridstack/gridstack@4.2.5/dist/gridstack-h5.js'];\n",
+ " const element = document.createElement(\"link\");\n",
+ " element.onload = on_load;\n",
+ " element.onerror = on_error;\n",
+ " element.rel = \"stylesheet\";\n",
+ " element.type = \"text/css\";\n",
+ " element.href = url;\n",
+ " console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n",
+ " document.body.appendChild(element);\n",
+ " } if (((window.Tabulator !== undefined) && (!(window.Tabulator instanceof HTMLElement))) || window.requirejs) {\n",
+ " var urls = ['https://cdn.holoviz.org/panel/1.4.2/dist/bundled/datatabulator/tabulator-tables@5.5.0/dist/js/tabulator.min.js'];\n",
" for (var i = 0; i < urls.length; i++) {\n",
" skip.push(urls[i])\n",
" }\n",
- " } if (((window['Notyf'] !== undefined) && (!(window['Notyf'] instanceof HTMLElement))) || window.requirejs) {\n",
- " var urls = ['https://cdn.holoviz.org/panel/0.14.3/dist/bundled/notificationarea/notyf@3/notyf.min.js'];\n",
+ " } if (((window.moment !== undefined) && (!(window.moment instanceof HTMLElement))) || window.requirejs) {\n",
+ " var urls = ['https://cdn.holoviz.org/panel/1.4.2/dist/bundled/datatabulator/luxon/build/global/luxon.min.js'];\n",
" for (var i = 0; i < urls.length; i++) {\n",
" skip.push(urls[i])\n",
" }\n",
- " } for (var i = 0; i < js_urls.length; i++) {\n",
+ " } var existing_scripts = []\n",
+ " var scripts = document.getElementsByTagName('script')\n",
+ " for (var i = 0; i < scripts.length; i++) {\n",
+ " var script = scripts[i]\n",
+ " if (script.src != null) {\n",
+ "\texisting_scripts.push(script.src)\n",
+ " }\n",
+ " }\n",
+ " for (var i = 0; i < js_urls.length; i++) {\n",
" var url = js_urls[i];\n",
- " if (skip.indexOf(url) >= 0) {\n",
+ " if (skip.indexOf(url) !== -1 || existing_scripts.indexOf(url) !== -1) {\n",
"\tif (!window.requirejs) {\n",
"\t on_load();\n",
"\t}\n",
@@ -149,7 +155,7 @@
" }\n",
" for (var i = 0; i < js_modules.length; i++) {\n",
" var url = js_modules[i];\n",
- " if (skip.indexOf(url) >= 0) {\n",
+ " if (skip.indexOf(url) !== -1 || existing_scripts.indexOf(url) !== -1) {\n",
"\tif (!window.requirejs) {\n",
"\t on_load();\n",
"\t}\n",
@@ -164,6 +170,26 @@
" console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n",
" document.head.appendChild(element);\n",
" }\n",
+ " for (const name in js_exports) {\n",
+ " var url = js_exports[name];\n",
+ " if (skip.indexOf(url) >= 0 || root[name] != null) {\n",
+ "\tif (!window.requirejs) {\n",
+ "\t on_load();\n",
+ "\t}\n",
+ "\tcontinue;\n",
+ " }\n",
+ " var element = document.createElement('script');\n",
+ " element.onerror = on_error;\n",
+ " element.async = false;\n",
+ " element.type = \"module\";\n",
+ " console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n",
+ " element.textContent = `\n",
+ " import ${name} from \"${url}\"\n",
+ " window.${name} = ${name}\n",
+ " window._bokeh_on_load()\n",
+ " `\n",
+ " document.head.appendChild(element);\n",
+ " }\n",
" if (!js_urls.length && !js_modules.length) {\n",
" on_load()\n",
" }\n",
@@ -175,12 +201,11 @@
" document.body.appendChild(element);\n",
" }\n",
"\n",
- " var js_urls = [\"https://cdn.holoviz.org/panel/0.14.3/dist/bundled/datatabulator/tabulator-tables@5.3.2/dist/js/tabulator.js\", \"https://cdn.holoviz.org/panel/0.14.3/dist/bundled/datatabulator/luxon/build/global/luxon.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-2.4.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-2.4.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-2.4.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-2.4.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-2.4.3.min.js\", \"https://unpkg.com/@holoviz/panel@0.14.3/dist/panel.min.js\"];\n",
+ " var js_urls = [\"https://cdn.holoviz.org/panel/1.4.2/dist/bundled/datatabulator/tabulator-tables@5.5.0/dist/js/tabulator.min.js\", \"https://cdn.holoviz.org/panel/1.4.2/dist/bundled/datatabulator/luxon/build/global/luxon.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-3.4.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.4.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.4.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.4.1.min.js\", \"https://cdn.holoviz.org/panel/1.4.2/dist/panel.min.js\"];\n",
" var js_modules = [];\n",
- " var css_urls = [\"https://cdn.holoviz.org/panel/0.14.3/dist/bundled/datatabulator/tabulator-tables@5.3.2/dist/css/tabulator_simple.min.css\", \"https://cdn.holoviz.org/panel/0.14.3/dist/css/card.css\", \"https://cdn.holoviz.org/panel/0.14.3/dist/css/markdown.css\", \"https://cdn.holoviz.org/panel/0.14.3/dist/css/widgets.css\", \"https://cdn.holoviz.org/panel/0.14.3/dist/css/loading.css\", \"https://cdn.holoviz.org/panel/0.14.3/dist/css/alerts.css\", \"https://cdn.holoviz.org/panel/0.14.3/dist/css/debugger.css\", \"https://cdn.holoviz.org/panel/0.14.3/dist/css/dataframe.css\", \"https://cdn.holoviz.org/panel/0.14.3/dist/css/json.css\"];\n",
+ " var js_exports = {};\n",
+ " var css_urls = [\"https://cdn.holoviz.org/panel/1.4.2/dist/bundled/datatabulator/tabulator-tables@5.5.0/dist/css/tabulator_simple.min.css?v=1.4.2\"];\n",
" var inline_js = [ function(Bokeh) {\n",
- " inject_raw_css(\"\\n .bk.pn-loading.arc:before {\\n background-image: url(\\\"data:image/svg+xml;base64,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\\\");\\n background-size: auto calc(min(50%, 400px));\\n }\\n \");\n",
- " }, function(Bokeh) {\n",
" Bokeh.set_log_level(\"info\");\n",
" },\n",
"function(Bokeh) {} // ensure no trailing comma for IE\n",
@@ -189,27 +214,67 @@
" function run_inline_js() {\n",
" if ((root.Bokeh !== undefined) || (force === true)) {\n",
" for (var i = 0; i < inline_js.length; i++) {\n",
- " inline_js[i].call(root, root.Bokeh);\n",
+ "\ttry {\n",
+ " inline_js[i].call(root, root.Bokeh);\n",
+ "\t} catch(e) {\n",
+ "\t if (!reloading) {\n",
+ "\t throw e;\n",
+ "\t }\n",
+ "\t}\n",
+ " }\n",
+ " // Cache old bokeh versions\n",
+ " if (Bokeh != undefined && !reloading) {\n",
+ "\tvar NewBokeh = root.Bokeh;\n",
+ "\tif (Bokeh.versions === undefined) {\n",
+ "\t Bokeh.versions = new Map();\n",
+ "\t}\n",
+ "\tif (NewBokeh.version !== Bokeh.version) {\n",
+ "\t Bokeh.versions.set(NewBokeh.version, NewBokeh)\n",
+ "\t}\n",
+ "\troot.Bokeh = Bokeh;\n",
" }} else if (Date.now() < root._bokeh_timeout) {\n",
" setTimeout(run_inline_js, 100);\n",
" } else if (!root._bokeh_failed_load) {\n",
" console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n",
" root._bokeh_failed_load = true;\n",
" }\n",
+ " root._bokeh_is_initializing = false\n",
" }\n",
"\n",
- " if (root._bokeh_is_loading === 0) {\n",
- " console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n",
- " run_inline_js();\n",
- " } else {\n",
- " load_libs(css_urls, js_urls, js_modules, function() {\n",
- " console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n",
- " run_inline_js();\n",
- " });\n",
+ " function load_or_wait() {\n",
+ " // Implement a backoff loop that tries to ensure we do not load multiple\n",
+ " // versions of Bokeh and its dependencies at the same time.\n",
+ " // In recent versions we use the root._bokeh_is_initializing flag\n",
+ " // to determine whether there is an ongoing attempt to initialize\n",
+ " // bokeh, however for backward compatibility we also try to ensure\n",
+ " // that we do not start loading a newer (Panel>=1.0 and Bokeh>3) version\n",
+ " // before older versions are fully initialized.\n",
+ " if (root._bokeh_is_initializing && Date.now() > root._bokeh_timeout) {\n",
+ " root._bokeh_is_initializing = false;\n",
+ " root._bokeh_onload_callbacks = undefined;\n",
+ " console.log(\"Bokeh: BokehJS was loaded multiple times but one version failed to initialize.\");\n",
+ " load_or_wait();\n",
+ " } else if (root._bokeh_is_initializing || (typeof root._bokeh_is_initializing === \"undefined\" && root._bokeh_onload_callbacks !== undefined)) {\n",
+ " setTimeout(load_or_wait, 100);\n",
+ " } else {\n",
+ " root._bokeh_is_initializing = true\n",
+ " root._bokeh_onload_callbacks = []\n",
+ " var bokeh_loaded = Bokeh != null && (Bokeh.version === py_version || (Bokeh.versions !== undefined && Bokeh.versions.has(py_version)));\n",
+ " if (!reloading && !bokeh_loaded) {\n",
+ "\troot.Bokeh = undefined;\n",
+ " }\n",
+ " load_libs(css_urls, js_urls, js_modules, js_exports, function() {\n",
+ "\tconsole.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n",
+ "\trun_inline_js();\n",
+ " });\n",
+ " }\n",
" }\n",
+ " // Give older versions of the autoload script a head-start to ensure\n",
+ " // they initialize before we start loading newer version.\n",
+ " setTimeout(load_or_wait, 100)\n",
"}(window));"
],
- "application/vnd.holoviews_load.v0+json": "(function(root) {\n function now() {\n return new Date();\n }\n\n var force = true;\n\n if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n root._bokeh_onload_callbacks = [];\n root._bokeh_is_loading = undefined;\n }\n\n if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n root._bokeh_timeout = Date.now() + 5000;\n root._bokeh_failed_load = false;\n }\n\n function run_callbacks() {\n try {\n root._bokeh_onload_callbacks.forEach(function(callback) {\n if (callback != null)\n callback();\n });\n } finally {\n delete root._bokeh_onload_callbacks\n }\n console.debug(\"Bokeh: all callbacks have finished\");\n }\n\n function load_libs(css_urls, js_urls, js_modules, callback) {\n if (css_urls == null) css_urls = [];\n if (js_urls == null) js_urls = [];\n if (js_modules == null) js_modules = [];\n\n root._bokeh_onload_callbacks.push(callback);\n if (root._bokeh_is_loading > 0) {\n console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n return null;\n }\n if (js_urls.length === 0 && js_modules.length === 0) {\n run_callbacks();\n return null;\n }\n console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n\n function on_load() {\n root._bokeh_is_loading--;\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n run_callbacks()\n }\n }\n\n function on_error() {\n console.error(\"failed to load \" + url);\n }\n\n for (var i = 0; i < css_urls.length; i++) {\n var url = css_urls[i];\n const element = document.createElement(\"link\");\n element.onload = on_load;\n element.onerror = on_error;\n element.rel = \"stylesheet\";\n element.type = \"text/css\";\n element.href = url;\n console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n document.body.appendChild(element);\n }\n\n var skip = [];\n if (window.requirejs) {\n window.requirejs.config({'packages': {}, 'paths': {'tabulator': 'https://cdn.jsdelivr.net/npm/tabulator-tables@5.3.2/dist/js/tabulator', 'moment': 'https://cdn.jsdelivr.net/npm/luxon/build/global/luxon.min', 'gridstack': 'https://cdn.jsdelivr.net/npm/gridstack@4.2.5/dist/gridstack-h5', 'notyf': 'https://cdn.jsdelivr.net/npm/notyf@3/notyf.min'}, 'shim': {'gridstack': {'exports': 'GridStack'}}});\n require([\"tabulator\"], function(Tabulator) {\n\twindow.Tabulator = Tabulator\n\ton_load()\n })\n require([\"moment\"], function(moment) {\n\twindow.moment = moment\n\ton_load()\n })\n require([\"gridstack\"], function(GridStack) {\n\twindow.GridStack = GridStack\n\ton_load()\n })\n require([\"notyf\"], function() {\n\ton_load()\n })\n root._bokeh_is_loading = css_urls.length + 4;\n } else {\n root._bokeh_is_loading = css_urls.length + js_urls.length + js_modules.length;\n } if (((window['Tabulator'] !== undefined) && (!(window['Tabulator'] instanceof HTMLElement))) || window.requirejs) {\n var urls = ['https://cdn.holoviz.org/panel/0.14.3/dist/bundled/datatabulator/tabulator-tables@5.3.2/dist/js/tabulator.js'];\n for (var i = 0; i < urls.length; i++) {\n skip.push(urls[i])\n }\n } if (((window['moment'] !== undefined) && (!(window['moment'] instanceof HTMLElement))) || window.requirejs) {\n var urls = ['https://cdn.holoviz.org/panel/0.14.3/dist/bundled/datatabulator/luxon/build/global/luxon.min.js'];\n for (var i = 0; i < urls.length; i++) {\n skip.push(urls[i])\n }\n } if (((window['GridStack'] !== undefined) && (!(window['GridStack'] instanceof HTMLElement))) || window.requirejs) {\n var urls = ['https://cdn.holoviz.org/panel/0.14.3/dist/bundled/gridstack/gridstack@4.2.5/dist/gridstack-h5.js'];\n for (var i = 0; i < urls.length; i++) {\n skip.push(urls[i])\n }\n } if (((window['Notyf'] !== undefined) && (!(window['Notyf'] instanceof HTMLElement))) || window.requirejs) {\n var urls = ['https://cdn.holoviz.org/panel/0.14.3/dist/bundled/notificationarea/notyf@3/notyf.min.js'];\n for (var i = 0; i < urls.length; i++) {\n skip.push(urls[i])\n }\n } for (var i = 0; i < js_urls.length; i++) {\n var url = js_urls[i];\n if (skip.indexOf(url) >= 0) {\n\tif (!window.requirejs) {\n\t on_load();\n\t}\n\tcontinue;\n }\n var element = document.createElement('script');\n element.onload = on_load;\n element.onerror = on_error;\n element.async = false;\n element.src = url;\n console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n document.head.appendChild(element);\n }\n for (var i = 0; i < js_modules.length; i++) {\n var url = js_modules[i];\n if (skip.indexOf(url) >= 0) {\n\tif (!window.requirejs) {\n\t on_load();\n\t}\n\tcontinue;\n }\n var element = document.createElement('script');\n element.onload = on_load;\n element.onerror = on_error;\n element.async = false;\n element.src = url;\n element.type = \"module\";\n console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n document.head.appendChild(element);\n }\n if (!js_urls.length && !js_modules.length) {\n on_load()\n }\n };\n\n function inject_raw_css(css) {\n const element = document.createElement(\"style\");\n element.appendChild(document.createTextNode(css));\n document.body.appendChild(element);\n }\n\n var js_urls = [\"https://cdn.holoviz.org/panel/0.14.3/dist/bundled/datatabulator/tabulator-tables@5.3.2/dist/js/tabulator.js\", \"https://cdn.holoviz.org/panel/0.14.3/dist/bundled/datatabulator/luxon/build/global/luxon.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-2.4.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-2.4.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-2.4.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-2.4.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-2.4.3.min.js\", \"https://unpkg.com/@holoviz/panel@0.14.3/dist/panel.min.js\"];\n var js_modules = [];\n var css_urls = [\"https://cdn.holoviz.org/panel/0.14.3/dist/bundled/datatabulator/tabulator-tables@5.3.2/dist/css/tabulator_simple.min.css\", \"https://cdn.holoviz.org/panel/0.14.3/dist/css/card.css\", \"https://cdn.holoviz.org/panel/0.14.3/dist/css/markdown.css\", \"https://cdn.holoviz.org/panel/0.14.3/dist/css/widgets.css\", \"https://cdn.holoviz.org/panel/0.14.3/dist/css/loading.css\", \"https://cdn.holoviz.org/panel/0.14.3/dist/css/alerts.css\", \"https://cdn.holoviz.org/panel/0.14.3/dist/css/debugger.css\", \"https://cdn.holoviz.org/panel/0.14.3/dist/css/dataframe.css\", \"https://cdn.holoviz.org/panel/0.14.3/dist/css/json.css\"];\n var inline_js = [ function(Bokeh) {\n inject_raw_css(\"\\n .bk.pn-loading.arc:before {\\n background-image: url(\\\"data:image/svg+xml;base64,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\\\");\\n background-size: auto calc(min(50%, 400px));\\n }\\n \");\n }, function(Bokeh) {\n Bokeh.set_log_level(\"info\");\n },\nfunction(Bokeh) {} // ensure no trailing comma for IE\n ];\n\n function run_inline_js() {\n if ((root.Bokeh !== undefined) || (force === true)) {\n for (var i = 0; i < inline_js.length; i++) {\n inline_js[i].call(root, root.Bokeh);\n }} else if (Date.now() < root._bokeh_timeout) {\n setTimeout(run_inline_js, 100);\n } else if (!root._bokeh_failed_load) {\n console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n root._bokeh_failed_load = true;\n }\n }\n\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n run_inline_js();\n } else {\n load_libs(css_urls, js_urls, js_modules, function() {\n console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n run_inline_js();\n });\n }\n}(window));"
+ "application/vnd.holoviews_load.v0+json": "(function(root) {\n function now() {\n return new Date();\n }\n\n var force = true;\n var py_version = '3.4.1'.replace('rc', '-rc.').replace('.dev', '-dev.');\n var reloading = false;\n var Bokeh = root.Bokeh;\n\n if (typeof (root._bokeh_timeout) === \"undefined\" || force) {\n root._bokeh_timeout = Date.now() + 5000;\n root._bokeh_failed_load = false;\n }\n\n function run_callbacks() {\n try {\n root._bokeh_onload_callbacks.forEach(function(callback) {\n if (callback != null)\n callback();\n });\n } finally {\n delete root._bokeh_onload_callbacks;\n }\n console.debug(\"Bokeh: all callbacks have finished\");\n }\n\n function load_libs(css_urls, js_urls, js_modules, js_exports, callback) {\n if (css_urls == null) css_urls = [];\n if (js_urls == null) js_urls = [];\n if (js_modules == null) js_modules = [];\n if (js_exports == null) js_exports = {};\n\n root._bokeh_onload_callbacks.push(callback);\n\n if (root._bokeh_is_loading > 0) {\n console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n return null;\n }\n if (js_urls.length === 0 && js_modules.length === 0 && Object.keys(js_exports).length === 0) {\n run_callbacks();\n return null;\n }\n if (!reloading) {\n console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n }\n\n function on_load() {\n root._bokeh_is_loading--;\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n run_callbacks()\n }\n }\n window._bokeh_on_load = on_load\n\n function on_error() {\n console.error(\"failed to load \" + url);\n }\n\n var skip = [];\n if (window.requirejs) {\n window.requirejs.config({'packages': {}, 'paths': {'tabulator': 'https://cdn.jsdelivr.net/npm/tabulator-tables@5.5.0/dist/js/tabulator.min', 'moment': 'https://cdn.jsdelivr.net/npm/luxon/build/global/luxon.min'}, 'shim': {}});\n require([\"tabulator\"], function(Tabulator) {\n\twindow.Tabulator = Tabulator\n\ton_load()\n })\n require([\"moment\"], function(moment) {\n\twindow.moment = moment\n\ton_load()\n })\n root._bokeh_is_loading = css_urls.length + 2;\n } else {\n root._bokeh_is_loading = css_urls.length + js_urls.length + js_modules.length + Object.keys(js_exports).length;\n }\n\n var existing_stylesheets = []\n var links = document.getElementsByTagName('link')\n for (var i = 0; i < links.length; i++) {\n var link = links[i]\n if (link.href != null) {\n\texisting_stylesheets.push(link.href)\n }\n }\n for (var i = 0; i < css_urls.length; i++) {\n var url = css_urls[i];\n if (existing_stylesheets.indexOf(url) !== -1) {\n\ton_load()\n\tcontinue;\n }\n const element = document.createElement(\"link\");\n element.onload = on_load;\n element.onerror = on_error;\n element.rel = \"stylesheet\";\n element.type = \"text/css\";\n element.href = url;\n console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n document.body.appendChild(element);\n } if (((window.Tabulator !== undefined) && (!(window.Tabulator instanceof HTMLElement))) || window.requirejs) {\n var urls = ['https://cdn.holoviz.org/panel/1.4.2/dist/bundled/datatabulator/tabulator-tables@5.5.0/dist/js/tabulator.min.js'];\n for (var i = 0; i < urls.length; i++) {\n skip.push(urls[i])\n }\n } if (((window.moment !== undefined) && (!(window.moment instanceof HTMLElement))) || window.requirejs) {\n var urls = ['https://cdn.holoviz.org/panel/1.4.2/dist/bundled/datatabulator/luxon/build/global/luxon.min.js'];\n for (var i = 0; i < urls.length; i++) {\n skip.push(urls[i])\n }\n } var existing_scripts = []\n var scripts = document.getElementsByTagName('script')\n for (var i = 0; i < scripts.length; i++) {\n var script = scripts[i]\n if (script.src != null) {\n\texisting_scripts.push(script.src)\n }\n }\n for (var i = 0; i < js_urls.length; i++) {\n var url = js_urls[i];\n if (skip.indexOf(url) !== -1 || existing_scripts.indexOf(url) !== -1) {\n\tif (!window.requirejs) {\n\t on_load();\n\t}\n\tcontinue;\n }\n var element = document.createElement('script');\n element.onload = on_load;\n element.onerror = on_error;\n element.async = false;\n element.src = url;\n console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n document.head.appendChild(element);\n }\n for (var i = 0; i < js_modules.length; i++) {\n var url = js_modules[i];\n if (skip.indexOf(url) !== -1 || existing_scripts.indexOf(url) !== -1) {\n\tif (!window.requirejs) {\n\t on_load();\n\t}\n\tcontinue;\n }\n var element = document.createElement('script');\n element.onload = on_load;\n element.onerror = on_error;\n element.async = false;\n element.src = url;\n element.type = \"module\";\n console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n document.head.appendChild(element);\n }\n for (const name in js_exports) {\n var url = js_exports[name];\n if (skip.indexOf(url) >= 0 || root[name] != null) {\n\tif (!window.requirejs) {\n\t on_load();\n\t}\n\tcontinue;\n }\n var element = document.createElement('script');\n element.onerror = on_error;\n element.async = false;\n element.type = \"module\";\n console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n element.textContent = `\n import ${name} from \"${url}\"\n window.${name} = ${name}\n window._bokeh_on_load()\n `\n document.head.appendChild(element);\n }\n if (!js_urls.length && !js_modules.length) {\n on_load()\n }\n };\n\n function inject_raw_css(css) {\n const element = document.createElement(\"style\");\n element.appendChild(document.createTextNode(css));\n document.body.appendChild(element);\n }\n\n var js_urls = [\"https://cdn.holoviz.org/panel/1.4.2/dist/bundled/datatabulator/tabulator-tables@5.5.0/dist/js/tabulator.min.js\", \"https://cdn.holoviz.org/panel/1.4.2/dist/bundled/datatabulator/luxon/build/global/luxon.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-3.4.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.4.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.4.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.4.1.min.js\", \"https://cdn.holoviz.org/panel/1.4.2/dist/panel.min.js\"];\n var js_modules = [];\n var js_exports = {};\n var css_urls = [\"https://cdn.holoviz.org/panel/1.4.2/dist/bundled/datatabulator/tabulator-tables@5.5.0/dist/css/tabulator_simple.min.css?v=1.4.2\"];\n var inline_js = [ function(Bokeh) {\n Bokeh.set_log_level(\"info\");\n },\nfunction(Bokeh) {} // ensure no trailing comma for IE\n ];\n\n function run_inline_js() {\n if ((root.Bokeh !== undefined) || (force === true)) {\n for (var i = 0; i < inline_js.length; i++) {\n\ttry {\n inline_js[i].call(root, root.Bokeh);\n\t} catch(e) {\n\t if (!reloading) {\n\t throw e;\n\t }\n\t}\n }\n // Cache old bokeh versions\n if (Bokeh != undefined && !reloading) {\n\tvar NewBokeh = root.Bokeh;\n\tif (Bokeh.versions === undefined) {\n\t Bokeh.versions = new Map();\n\t}\n\tif (NewBokeh.version !== Bokeh.version) {\n\t Bokeh.versions.set(NewBokeh.version, NewBokeh)\n\t}\n\troot.Bokeh = Bokeh;\n }} else if (Date.now() < root._bokeh_timeout) {\n setTimeout(run_inline_js, 100);\n } else if (!root._bokeh_failed_load) {\n console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n root._bokeh_failed_load = true;\n }\n root._bokeh_is_initializing = false\n }\n\n function load_or_wait() {\n // Implement a backoff loop that tries to ensure we do not load multiple\n // versions of Bokeh and its dependencies at the same time.\n // In recent versions we use the root._bokeh_is_initializing flag\n // to determine whether there is an ongoing attempt to initialize\n // bokeh, however for backward compatibility we also try to ensure\n // that we do not start loading a newer (Panel>=1.0 and Bokeh>3) version\n // before older versions are fully initialized.\n if (root._bokeh_is_initializing && Date.now() > root._bokeh_timeout) {\n root._bokeh_is_initializing = false;\n root._bokeh_onload_callbacks = undefined;\n console.log(\"Bokeh: BokehJS was loaded multiple times but one version failed to initialize.\");\n load_or_wait();\n } else if (root._bokeh_is_initializing || (typeof root._bokeh_is_initializing === \"undefined\" && root._bokeh_onload_callbacks !== undefined)) {\n setTimeout(load_or_wait, 100);\n } else {\n root._bokeh_is_initializing = true\n root._bokeh_onload_callbacks = []\n var bokeh_loaded = Bokeh != null && (Bokeh.version === py_version || (Bokeh.versions !== undefined && Bokeh.versions.has(py_version)));\n if (!reloading && !bokeh_loaded) {\n\troot.Bokeh = undefined;\n }\n load_libs(css_urls, js_urls, js_modules, js_exports, function() {\n\tconsole.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n\trun_inline_js();\n });\n }\n }\n // Give older versions of the autoload script a head-start to ensure\n // they initialize before we start loading newer version.\n setTimeout(load_or_wait, 100)\n}(window));"
},
"metadata": {},
"output_type": "display_data"
@@ -465,16 +530,104 @@
{
"data": {
"text/html": [
- ""
]
},
"metadata": {},
"output_type": "display_data"
+ },
+ {
+ "data": {
+ "application/vnd.holoviews_exec.v0+json": "",
+ "text/html": [
+ "\n",
+ ""
+ ]
+ },
+ "metadata": {
+ "application/vnd.holoviews_exec.v0+json": {
+ "id": "192c6cb1-7fb4-45b3-9d1a-8b03f38b7639"
+ }
+ },
+ "output_type": "display_data"
}
],
"source": [
@@ -522,10 +675,8 @@
},
{
"cell_type": "code",
- "execution_count": 2,
- "metadata": {
- "scrolled": false
- },
+ "execution_count": 7,
+ "metadata": {},
"outputs": [
{
"data": {
@@ -542,7 +693,7 @@
{
"data": {
"application/vnd.jupyter.widget-view+json": {
- "model_id": "2d50569d860f4a0cb21897574102b3c6",
+ "model_id": "2591a5847c4d4c6c800c6a346d034116",
"version_major": 2,
"version_minor": 0
},
@@ -556,7 +707,7 @@
{
"data": {
"application/vnd.jupyter.widget-view+json": {
- "model_id": "31fbc31f68654595a8256a3056752f6c",
+ "model_id": "a8c1213493474283b20176bc0182370a",
"version_major": 2,
"version_minor": 0
},
@@ -570,7 +721,7 @@
{
"data": {
"application/vnd.jupyter.widget-view+json": {
- "model_id": "b936e7b716f94cc9acdf6edb4efd698d",
+ "model_id": "600825a6a8e2473cb81d61516a173349",
"version_major": 2,
"version_minor": 0
},
@@ -620,13 +771,13 @@
},
{
"cell_type": "code",
- "execution_count": 3,
+ "execution_count": 8,
"metadata": {},
"outputs": [
{
"data": {
"application/vnd.jupyter.widget-view+json": {
- "model_id": "edeff71abf6e4316a191b84e8c930ea5",
+ "model_id": "6f2d476c6c614a69b737fab48247e58a",
"version_major": 2,
"version_minor": 0
},
@@ -640,7 +791,7 @@
{
"data": {
"application/vnd.jupyter.widget-view+json": {
- "model_id": "098cd7acfa9b46739994b1492e713f33",
+ "model_id": "2478f02c00724be0aba616bd135cc974",
"version_major": 2,
"version_minor": 0
},
@@ -654,7 +805,7 @@
{
"data": {
"application/vnd.jupyter.widget-view+json": {
- "model_id": "1ed41c90dc3642daadb08ca93a7e9147",
+ "model_id": "5a39454270114ece830aeb5222873dd4",
"version_major": 2,
"version_minor": 0
},
@@ -670,6 +821,13 @@
"widgetSave = SaveWidget()\n",
"widgetSave.display_widgets()\n"
]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": []
}
],
"metadata": {
@@ -688,7 +846,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.8.18"
+ "version": "3.12.4"
}
},
"nbformat": 4,
diff --git a/src/image_widget_all_ch.py b/src/image_widget_all_ch.py
index 14f770f..17dc3d0 100644
--- a/src/image_widget_all_ch.py
+++ b/src/image_widget_all_ch.py
@@ -236,7 +236,7 @@ def __init__(self):
# Define widgets
self.btn_saving_options = widgets.Button(description='Saving Options')
self.btn_saving_options.on_click(self._update_output)
- self.btn_saving_options.on_click(self._saving_options_eventhandler)
+ # self.btn_saving_options.on_click(self._saving_options_eventhandler)
self.PATH = widgets.Text(value='path/to/data', description='Original Path:', disabled=False)
# self.button = widgets.Button(description="Change Path")
# self.button.on_click(self._update_output)
@@ -311,43 +311,58 @@ def save_imgs(self, binary_masks=False):
if not os.path.exists(self.txtbox.value):
os.makedirs(self.txtbox.value)
- # does all the files
+
+ # Process images
images_original, imgs_norm = JN.preprocess_images_pages(self.files)
imgs_channel = [images_original[i] for i in range(len(images_original))]
norm_imgs_channel = [imgs_norm[i] for i in range(len(imgs_norm))]
- # grab the th_list and the percentile_list
+ # Grab the th_list and the percentile_list
download_table = self.edit_table
th_list = list(download_table.value['threshold'])
percentile_list = list(download_table.value['percentile'])
+ # Save parameters to CSV
csv_path = os.path.join(str(self.path_for_results), 'denoiseParameters.csv')
- # download_table.download(csv_path) # download in the wrong folder
-
df = pd.DataFrame(download_table.value)
df.to_csv(csv_path, index=True)
+ # Filter images
imgs_filtered = map(lambda i: JN.calculus_multitiff_lists(i, th_list, percentile_list), norm_imgs_channel)
imgs_filtered = list(imgs_filtered)
if binary_masks:
imgs_filtered = [np.where(a > 0, 1, 0) for a in imgs_filtered]
- # get the names of images
- names_save = [str(self.path_for_results + sub) for sub in self.images_names]
+ # Save images individually in their respective folders
+ for i, file_name in enumerate(self.files):
+ # Create a folder for each file
+ file_base_name = os.path.splitext(os.path.basename(file_name))[0]
+ folder_path = os.path.join(self.txtbox.value, file_base_name)
+ if not os.path.exists(folder_path):
+ os.makedirs(folder_path)
- if isinstance(self.channel_names[0], str):
- images_final = map(
- lambda p, f: IPrep.save_img_ch_names_pages(p, f, ch_last=True, channel_names=self.channel_names),
- imgs_filtered, names_save)
-
- else:
- # will not save channel names
- images_final = map(lambda p, f: IPrep.save_images(p, f, ch_last=True), imgs_filtered, names_save)
+ # Get the image to save
+ img_to_save = imgs_filtered[i] # Assuming one image per file
- it = list(images_final)
- print(f'Images saved at {self.path_for_results}')
+ # Define the path to save the image
+ save_path = os.path.join(folder_path, f"{file_base_name}.tiff")
+ # Save the image
+ if isinstance(self.channel_names[0], str):
+ IPrep.save_img_ch_names_pages(img_to_save, save_path, ch_last=True, channel_names=self.channel_names)
+ else:
+ IPrep.save_images(img_to_save, save_path, ch_last=True)
+
+ # Create 'tiles.txt' file with a '0' inside
+ txt_file_path = os.path.join(folder_path, 'Tiles.txt')
+ with open(txt_file_path, 'w') as f:
+ f.write('0')
+
+ if self.output_widget:
+ self.output_widget.append_stdout(f'Images saved in {self.txtbox.value}\n')
+ else:
+ print(f'Images saved in {self.txtbox.value}')
def _update_output(self, button):
with self.output_widget:
@@ -360,6 +375,8 @@ def _update_output(self, button):
print("Path provided:", directory_path)
self.folder_path = directory_path
self._load_files_from_folder(directory_path)
+ self._saving_options_eventhandler(button) # Call the method here
+
else:
print("Error: The specified directory is empty.")
else: