From 027a8d67f1395aff7ef5d872d9ed535ed57e596c Mon Sep 17 00:00:00 2001
From: Hamish Graham <hgraham@hpc-201-11-01-a.cr.cnaf.infn.it>
Date: Mon, 30 Aug 2021 14:15:52 +0200
Subject: [PATCH] updated pandas_with_bokeh
---
examples/hamish_example/pandas_bokeh.py | 55 +
examples/hamish_example/pandas_skeleton.py | 104 ++
.../hamish_example/pandas_with_bokeh.ipynb | 1262 +++++++++++++++++
3 files changed, 1421 insertions(+)
create mode 100644 examples/hamish_example/pandas_bokeh.py
create mode 100644 examples/hamish_example/pandas_skeleton.py
create mode 100644 examples/hamish_example/pandas_with_bokeh.ipynb
diff --git a/examples/hamish_example/pandas_bokeh.py b/examples/hamish_example/pandas_bokeh.py
new file mode 100644
index 0000000..89d802a
--- /dev/null
+++ b/examples/hamish_example/pandas_bokeh.py
@@ -0,0 +1,55 @@
+import pandas_skeleton as ps
+import tree_maker as tm
+from pandas import DataFrame
+
+from bokeh.layouts import column
+from bokeh.models import ColumnDataSource, Slider, WheelZoomTool, BoxZoomTool, Button
+from bokeh.plotting import figure
+from bokeh.themes import Theme
+from bokeh.io import show, output_notebook
+
+output_notebook()
+
+#root = tm.tree_from_json(filename='/home/HPC/sterbini/DA_study_example/study_000/tree.json')
+
+def bkapp(doc):
+ global my_df
+ global source
+
+ try:
+ ps.create_tree(root)
+ except:
+ raise Exception('Sorry, I need a root of a tree!')
+
+ x_values, y_values, path = ps.create_xypath(root)
+ my_colors = ps.create_color(root)
+ angles = ps.create_tree_cartesian(root)
+
+ my_df = ps.create_df(root, path, x_values, y_values, my_colors)
+
+ del my_df['handle']
+
+ source = ColumnDataSource(data=my_df)
+
+ plot = figure(plot_width=400, plot_height=400, tools="lasso_select", title="Select Here")
+ plot.circle('x', 'y', source=source, alpha=0.6, color = 'color')
+ plot.add_tools(BoxZoomTool())
+
+ def callback(attr, index_list, _):
+ global my_df
+ global my_df_selected
+ source.data = ColumnDataSource.from_df(my_df)
+ my_df_selected = my_df.loc[index_list]
+
+ def dummyfunction():
+ global my_df
+ my_df = ps.update(my_df, 'completed', 'green')
+
+ source.selected.on_change('indices', callback)
+ button = Button(label="Update", button_type="success")
+
+ button.on_click(dummyfunction)
+
+ doc.add_root(column(plot, button))
+
+show(bkapp, notebook_url='http://localhost:8102', port=8202) # notebook_url="http://localhost:8888"
\ No newline at end of file
diff --git a/examples/hamish_example/pandas_skeleton.py b/examples/hamish_example/pandas_skeleton.py
new file mode 100644
index 0000000..4626973
--- /dev/null
+++ b/examples/hamish_example/pandas_skeleton.py
@@ -0,0 +1,104 @@
+import tree_maker as tm
+import numpy as np
+import math
+import random
+from anytree import AnyNode, RenderTree
+import numpy as np
+import json
+import pandas as pd
+
+def create_tree(node):
+ """
+ Creates a tree with the shape of a 'flower'. The nodes that have attributes; x, y, ragius, short_path, angle, min_angle, max_angle and color.
+ """
+ if node.is_leaf:
+ pass
+ else:
+ if node.is_root:
+ node.x = 0
+ node.y = 0
+ node.radius = 0
+ #node.min_x = -2
+ #node.max_x = 2
+ node.short_path = '/'.join(node.path.split('/')[-3:])
+ node.angle = 2 * math.pi
+ node.min_angle = 0
+ node.max_angle = 2 * math.pi
+ node.color = 'black'
+ for my_child, my_angle in zip(node.children, np.linspace(node.min_angle, node.max_angle, len(node.children))):
+ #my_child.min_x = xx - (node.max_x - node.min_x)/len(node.children)/2
+ #my_child.max_x = xx + (node.max_x - node.min_x)/len(node.children)/2
+ my_child.color = "black"
+ my_child.short_path = '/'.join(my_child.path.split('/')[-3:])
+ my_child.angle = my_angle
+ my_child.min_angle = my_angle - (node.max_angle - node.min_angle)/len(node.children)/2
+ my_child.max_angle = my_angle + (node.max_angle - node.min_angle)/len(node.children)/2
+ my_child.radius = node.radius + 1
+ my_child.x = my_child.radius * math.cos(my_angle)
+ my_child.y = my_child.radius * math.sin(my_angle)
+ create_tree(my_child)
+
+
+def create_xypath(node):
+ """
+ Creates a list for x_values and y_values for the nodes of a tree.
+ """
+ x_values = [node.x]
+ y_values = [node.y]
+ path = [node.short_path]
+ for descendant in node.descendants:
+ x_values.append(descendant.x)
+ y_values.append(descendant.y)
+ path.append(descendant.short_path)
+ return x_values, y_values, path
+
+def create_color(node):
+ """
+ Adds colors of nodes to an array.
+ """
+ my_colors = [node.color]
+ for descendant in node.descendants:
+ my_colors.append(descendant.color)
+ return my_colors
+
+def create_tree_cartesian(node):
+ """
+ Adds the angle attribute to an array.
+ """
+ angles = [node.angle]
+ for descendant in node.descendants:
+ angles.append(node.angle)
+ return angles
+
+def get_status(handle):
+ """
+ Returns last key, the status of the job, from 'log_file'. Incase of an empty log_file, 'None' is returned.
+ """
+ keys = list(tm.from_json(handle.log_file))
+ if len(keys) > 0:
+ return keys[-1]
+ else:
+ return None
+
+def create_df(node, path, x_values, y_values, my_colors):
+ """
+ Creating a dataframe and its attributes. Here its attributes are; node, path, x_values, y_values and my_colors.
+ """
+ my_df = pd.DataFrame([node]+list(node.descendants), columns=['handle']).copy()
+ my_df['name'] = my_df['handle'].apply(lambda x:x.name)
+ my_df['path'] = path
+ my_df['x'] = x_values # to check the order
+ my_df['y'] = y_values # to check the order
+ my_df['status'] = my_df['handle'].apply(get_status)
+ my_df['color'] = my_colors
+ return my_df
+
+def update(my_df, last_key, my_color):
+ """
+ Filtering through the dataframe using the 'last_key'. The color that is connected to this 'last_key', can also be chosen.
+ """
+ new_df1 = my_df[(my_df.status == last_key)].copy()
+ new_df1['color'] = my_color
+ new_df2 = my_df[(my_df.status != last_key)].copy()
+ my_df = pd.concat([new_df1, new_df2]).sort_index()
+ return my_df
\ No newline at end of file
diff --git a/examples/hamish_example/pandas_with_bokeh.ipynb b/examples/hamish_example/pandas_with_bokeh.ipynb
new file mode 100644
index 0000000..adf98c7
--- /dev/null
+++ b/examples/hamish_example/pandas_with_bokeh.ipynb
@@ -0,0 +1,1262 @@
+{
+ "cells": [
+ {
+ "cell_type": "code",
+ "execution_count": 1,
+ "id": "7f7bb5b9-554d-45b0-b7b5-6e0240c836c5",
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ " <div class=\"bk-root\">\n",
+ " <a href=\"https://bokeh.org\" target=\"_blank\" class=\"bk-logo bk-logo-small bk-logo-notebook\"></a>\n",
+ " <span id=\"1002\">Loading BokehJS ...</span>\n",
+ " </div>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "application/javascript": [
+ "\n",
+ "(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",
+ " var JS_MIME_TYPE = 'application/javascript';\n",
+ " var HTML_MIME_TYPE = 'text/html';\n",
+ " var EXEC_MIME_TYPE = 'application/vnd.bokehjs_exec.v0+json';\n",
+ " var CLASS_NAME = 'output_bokeh rendered_html';\n",
+ "\n",
+ " /**\n",
+ " * Render data to the DOM node\n",
+ " */\n",
+ " function render(props, node) {\n",
+ " var script = document.createElement(\"script\");\n",
+ " node.appendChild(script);\n",
+ " }\n",
+ "\n",
+ " /**\n",
+ " * Handle when an output is cleared or removed\n",
+ " */\n",
+ " function handleClearOutput(event, handle) {\n",
+ " var cell = handle.cell;\n",
+ "\n",
+ " var id = cell.output_area._bokeh_element_id;\n",
+ " var server_id = cell.output_area._bokeh_server_id;\n",
+ " // Clean up Bokeh references\n",
+ " if (id != null && id in Bokeh.index) {\n",
+ " Bokeh.index[id].model.document.clear();\n",
+ " delete Bokeh.index[id];\n",
+ " }\n",
+ "\n",
+ " if (server_id !== undefined) {\n",
+ " // Clean up Bokeh references\n",
+ " var cmd = \"from bokeh.io.state import curstate; print(curstate().uuid_to_server['\" + server_id + \"'].get_sessions()[0].document.roots[0]._id)\";\n",
+ " cell.notebook.kernel.execute(cmd, {\n",
+ " iopub: {\n",
+ " output: function(msg) {\n",
+ " var id = msg.content.text.trim();\n",
+ " if (id in Bokeh.index) {\n",
+ " Bokeh.index[id].model.document.clear();\n",
+ " delete Bokeh.index[id];\n",
+ " }\n",
+ " }\n",
+ " }\n",
+ " });\n",
+ " // Destroy server and session\n",
+ " var cmd = \"import bokeh.io.notebook as ion; ion.destroy_server('\" + server_id + \"')\";\n",
+ " cell.notebook.kernel.execute(cmd);\n",
+ " }\n",
+ " }\n",
+ "\n",
+ " /**\n",
+ " * Handle when a new output is added\n",
+ " */\n",
+ " function handleAddOutput(event, handle) {\n",
+ " var output_area = handle.output_area;\n",
+ " var output = handle.output;\n",
+ "\n",
+ " // limit handleAddOutput to display_data with EXEC_MIME_TYPE content only\n",
+ " if ((output.output_type != \"display_data\") || (!Object.prototype.hasOwnProperty.call(output.data, EXEC_MIME_TYPE))) {\n",
+ " return\n",
+ " }\n",
+ "\n",
+ " var toinsert = output_area.element.find(\".\" + CLASS_NAME.split(' ')[0]);\n",
+ "\n",
+ " if (output.metadata[EXEC_MIME_TYPE][\"id\"] !== undefined) {\n",
+ " toinsert[toinsert.length - 1].firstChild.textContent = output.data[JS_MIME_TYPE];\n",
+ " // store reference to embed id on output_area\n",
+ " output_area._bokeh_element_id = output.metadata[EXEC_MIME_TYPE][\"id\"];\n",
+ " }\n",
+ " if (output.metadata[EXEC_MIME_TYPE][\"server_id\"] !== undefined) {\n",
+ " var bk_div = document.createElement(\"div\");\n",
+ " bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n",
+ " var script_attrs = bk_div.children[0].attributes;\n",
+ " for (var i = 0; i < script_attrs.length; i++) {\n",
+ " toinsert[toinsert.length - 1].firstChild.setAttribute(script_attrs[i].name, script_attrs[i].value);\n",
+ " toinsert[toinsert.length - 1].firstChild.textContent = bk_div.children[0].textContent\n",
+ " }\n",
+ " // store reference to server id on output_area\n",
+ " output_area._bokeh_server_id = output.metadata[EXEC_MIME_TYPE][\"server_id\"];\n",
+ " }\n",
+ " }\n",
+ "\n",
+ " function register_renderer(events, OutputArea) {\n",
+ "\n",
+ " function append_mime(data, metadata, element) {\n",
+ " // create a DOM node to render to\n",
+ " var toinsert = this.create_output_subarea(\n",
+ " metadata,\n",
+ " CLASS_NAME,\n",
+ " EXEC_MIME_TYPE\n",
+ " );\n",
+ " this.keyboard_manager.register_events(toinsert);\n",
+ " // Render to node\n",
+ " var props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};\n",
+ " render(props, toinsert[toinsert.length - 1]);\n",
+ " element.append(toinsert);\n",
+ " return toinsert\n",
+ " }\n",
+ "\n",
+ " /* Handle when an output is cleared or removed */\n",
+ " events.on('clear_output.CodeCell', handleClearOutput);\n",
+ " events.on('delete.Cell', handleClearOutput);\n",
+ "\n",
+ " /* Handle when a new output is added */\n",
+ " events.on('output_added.OutputArea', handleAddOutput);\n",
+ "\n",
+ " /**\n",
+ " * Register the mime type and append_mime function with output_area\n",
+ " */\n",
+ " OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n",
+ " /* Is output safe? */\n",
+ " safe: true,\n",
+ " /* Index of renderer in `output_area.display_order` */\n",
+ " index: 0\n",
+ " });\n",
+ " }\n",
+ "\n",
+ " // register the mime type if in Jupyter Notebook environment and previously unregistered\n",
+ " if (root.Jupyter !== undefined) {\n",
+ " var events = require('base/js/events');\n",
+ " var OutputArea = require('notebook/js/outputarea').OutputArea;\n",
+ "\n",
+ " if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n",
+ " register_renderer(events, OutputArea);\n",
+ " }\n",
+ " }\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",
+ " var NB_LOAD_WARNING = {'data': {'text/html':\n",
+ " \"<div style='background-color: #fdd'>\\n\"+\n",
+ " \"<p>\\n\"+\n",
+ " \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n",
+ " \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n",
+ " \"</p>\\n\"+\n",
+ " \"<ul>\\n\"+\n",
+ " \"<li>re-rerun `output_notebook()` to attempt to load from CDN again, or</li>\\n\"+\n",
+ " \"<li>use INLINE resources instead, as so:</li>\\n\"+\n",
+ " \"</ul>\\n\"+\n",
+ " \"<code>\\n\"+\n",
+ " \"from bokeh.resources import INLINE\\n\"+\n",
+ " \"output_notebook(resources=INLINE)\\n\"+\n",
+ " \"</code>\\n\"+\n",
+ " \"</div>\"}};\n",
+ "\n",
+ " function display_loaded() {\n",
+ " var el = document.getElementById(\"1002\");\n",
+ " if (el != null) {\n",
+ " el.textContent = \"BokehJS is loading...\";\n",
+ " }\n",
+ " if (root.Bokeh !== undefined) {\n",
+ " if (el != null) {\n",
+ " el.textContent = \"BokehJS \" + root.Bokeh.version + \" successfully loaded.\";\n",
+ " }\n",
+ " } else if (Date.now() < root._bokeh_timeout) {\n",
+ " setTimeout(display_loaded, 100)\n",
+ " }\n",
+ " }\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, callback) {\n",
+ " if (css_urls == null) css_urls = [];\n",
+ " if (js_urls == null) js_urls = [];\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 == null || js_urls.length === 0) {\n",
+ " run_callbacks();\n",
+ " return null;\n",
+ " }\n",
+ " console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n",
+ " root._bokeh_is_loading = css_urls.length + js_urls.length;\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(url) {\n",
+ " console.error(\"failed to load \" + url);\n",
+ " }\n",
+ "\n",
+ " for (let i = 0; i < css_urls.length; i++) {\n",
+ " const url = css_urls[i];\n",
+ " const element = document.createElement(\"link\");\n",
+ " element.onload = on_load;\n",
+ " element.onerror = on_error.bind(null, url);\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",
+ " const hashes = {\"https://cdn.bokeh.org/bokeh/release/bokeh-2.3.3.min.js\": \"dM3QQsP+wXdHg42wTqW85BjZQdLNNIXqlPw/BgKoExPmTG7ZLML4EGqLMfqHT6ON\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-2.3.3.min.js\": \"8x57I4YuIfu8XyZfFo0XVr2WAT8EK4rh/uDe3wF7YuW2FNUSNEpJbsPaB1nJ2fz2\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-2.3.3.min.js\": \"3QTqdz9LyAm2i0sG5XTePsHec3UHWwVsrOL68SYRoAXsafvfAyqtQ+h440+qIBhS\"};\n",
+ "\n",
+ " for (let i = 0; i < js_urls.length; i++) {\n",
+ " const url = js_urls[i];\n",
+ " const element = document.createElement('script');\n",
+ " element.onload = on_load;\n",
+ " element.onerror = on_error.bind(null, url);\n",
+ " element.async = false;\n",
+ " element.src = url;\n",
+ " if (url in hashes) {\n",
+ " element.crossOrigin = \"anonymous\";\n",
+ " element.integrity = \"sha384-\" + hashes[url];\n",
+ " }\n",
+ " console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n",
+ " document.head.appendChild(element);\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",
+ " \n",
+ " var js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-2.3.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-2.3.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-2.3.3.min.js\"];\n",
+ " var css_urls = [];\n",
+ " \n",
+ "\n",
+ " var inline_js = [\n",
+ " function(Bokeh) {\n",
+ " Bokeh.set_log_level(\"info\");\n",
+ " },\n",
+ " function(Bokeh) {\n",
+ " \n",
+ " \n",
+ " }\n",
+ " ];\n",
+ "\n",
+ " function run_inline_js() {\n",
+ " \n",
+ " if (root.Bokeh !== undefined || force === true) {\n",
+ " \n",
+ " for (var i = 0; i < inline_js.length; i++) {\n",
+ " inline_js[i].call(root, root.Bokeh);\n",
+ " }\n",
+ " if (force === true) {\n",
+ " display_loaded();\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",
+ " } else if (force !== true) {\n",
+ " var cell = $(document.getElementById(\"1002\")).parents('.cell').data().cell;\n",
+ " cell.output_area.append_execute_result(NB_LOAD_WARNING)\n",
+ " }\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, function() {\n",
+ " console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n",
+ " run_inline_js();\n",
+ " });\n",
+ " }\n",
+ "}(window));"
+ ],
+ "application/vnd.bokehjs_load.v0+json": "\n(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 \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 var NB_LOAD_WARNING = {'data': {'text/html':\n \"<div style='background-color: #fdd'>\\n\"+\n \"<p>\\n\"+\n \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n \"</p>\\n\"+\n \"<ul>\\n\"+\n \"<li>re-rerun `output_notebook()` to attempt to load from CDN again, or</li>\\n\"+\n \"<li>use INLINE resources instead, as so:</li>\\n\"+\n \"</ul>\\n\"+\n \"<code>\\n\"+\n \"from bokeh.resources import INLINE\\n\"+\n \"output_notebook(resources=INLINE)\\n\"+\n \"</code>\\n\"+\n \"</div>\"}};\n\n function display_loaded() {\n var el = document.getElementById(\"1002\");\n if (el != null) {\n el.textContent = \"BokehJS is loading...\";\n }\n if (root.Bokeh !== undefined) {\n if (el != null) {\n el.textContent = \"BokehJS \" + root.Bokeh.version + \" successfully loaded.\";\n }\n } else if (Date.now() < root._bokeh_timeout) {\n setTimeout(display_loaded, 100)\n }\n }\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, callback) {\n if (css_urls == null) css_urls = [];\n if (js_urls == null) js_urls = [];\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 == null || js_urls.length === 0) {\n run_callbacks();\n return null;\n }\n console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n root._bokeh_is_loading = css_urls.length + js_urls.length;\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(url) {\n console.error(\"failed to load \" + url);\n }\n\n for (let i = 0; i < css_urls.length; i++) {\n const url = css_urls[i];\n const element = document.createElement(\"link\");\n element.onload = on_load;\n element.onerror = on_error.bind(null, url);\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 const hashes = {\"https://cdn.bokeh.org/bokeh/release/bokeh-2.3.3.min.js\": \"dM3QQsP+wXdHg42wTqW85BjZQdLNNIXqlPw/BgKoExPmTG7ZLML4EGqLMfqHT6ON\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-2.3.3.min.js\": \"8x57I4YuIfu8XyZfFo0XVr2WAT8EK4rh/uDe3wF7YuW2FNUSNEpJbsPaB1nJ2fz2\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-2.3.3.min.js\": \"3QTqdz9LyAm2i0sG5XTePsHec3UHWwVsrOL68SYRoAXsafvfAyqtQ+h440+qIBhS\"};\n\n for (let i = 0; i < js_urls.length; i++) {\n const url = js_urls[i];\n const element = document.createElement('script');\n element.onload = on_load;\n element.onerror = on_error.bind(null, url);\n element.async = false;\n element.src = url;\n if (url in hashes) {\n element.crossOrigin = \"anonymous\";\n element.integrity = \"sha384-\" + hashes[url];\n }\n console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n document.head.appendChild(element);\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 \n var js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-2.3.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-2.3.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-2.3.3.min.js\"];\n var css_urls = [];\n \n\n var inline_js = [\n function(Bokeh) {\n Bokeh.set_log_level(\"info\");\n },\n function(Bokeh) {\n \n \n }\n ];\n\n function run_inline_js() {\n \n if (root.Bokeh !== undefined || force === true) {\n \n for (var i = 0; i < inline_js.length; i++) {\n inline_js[i].call(root, root.Bokeh);\n }\n if (force === true) {\n display_loaded();\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 } else if (force !== true) {\n var cell = $(document.getElementById(\"1002\")).parents('.cell').data().cell;\n cell.output_area.append_execute_result(NB_LOAD_WARNING)\n }\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, function() {\n console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n run_inline_js();\n });\n }\n}(window));"
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "import pandas_skeleton as ps\n",
+ "import tree_maker as tm\n",
+ "from pandas import DataFrame\n",
+ "\n",
+ "from bokeh.layouts import column\n",
+ "from bokeh.models import ColumnDataSource, Slider, WheelZoomTool, BoxZoomTool, Button\n",
+ "from bokeh.plotting import figure\n",
+ "from bokeh.themes import Theme\n",
+ "from bokeh.io import show, output_notebook\n",
+ "\n",
+ "output_notebook()"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 2,
+ "id": "68380bba-2edd-4d18-b95d-57819da498b0",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "%load_ext autoreload"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 3,
+ "id": "f684f232-914a-4f2e-8835-a5c0b35576f6",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "%autoreload 2"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 4,
+ "id": "41e859af-98f5-492e-9c98-ec03cf59294a",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "root = tm.tree_from_json(filename='/home/HPC/sterbini/DA_study_example/study_000/tree.json')"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 8,
+ "id": "78cab292-371e-44dd-9d8e-50b6bd4f7b9e",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "def bkapp(doc):\n",
+ " #root = my_root\n",
+ " \n",
+ " global my_df\n",
+ " global source\n",
+ " ps.create_tree(root)\n",
+ " \n",
+ " x_values, y_values, path = ps.create_xypath(root)\n",
+ " my_colors = ps.create_color(root)\n",
+ " angles = ps.create_tree_cartesian(root)\n",
+ " \n",
+ " my_df = ps.create_df(root, path, x_values, y_values, my_colors)\n",
+ " \n",
+ " del my_df['handle']\n",
+ " \n",
+ " source = ColumnDataSource(data=my_df)\n",
+ "\n",
+ " plot = figure(plot_width=400, plot_height=400, tools=\"lasso_select\", title=\"Select Here\")\n",
+ " plot.circle('x', 'y', source=source, alpha=0.6, color = 'color')\n",
+ " plot.add_tools(BoxZoomTool())\n",
+ " \n",
+ " def callback(attr, index_list, _):\n",
+ " global my_df\n",
+ " global my_df_selected\n",
+ " source.data = ColumnDataSource.from_df(my_df)\n",
+ " my_df_selected = my_df.loc[index_list]\n",
+ "\n",
+ " def dummyfunction():\n",
+ " global my_df\n",
+ " my_df = ps.update(my_df, 'completed', 'green')\n",
+ "\n",
+ " source.selected.on_change('indices', callback)\n",
+ " button = Button(label=\"hello\", button_type=\"success\")\n",
+ "\n",
+ " button.on_click(dummyfunction)\n",
+ "\n",
+ " doc.add_root(column(plot, button))"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 9,
+ "id": "466ec80a-215a-4969-b876-b96a3ead3994",
+ "metadata": {},
+ "outputs": [
+ {
+ "ename": "OSError",
+ "evalue": "[Errno 98] Address already in use",
+ "output_type": "error",
+ "traceback": [
+ "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+ "\u001b[0;31mOSError\u001b[0m Traceback (most recent call last)",
+ "\u001b[0;32m/tmp/ipykernel_25955/1803267195.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mshow\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mbkapp\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mnotebook_url\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m'http://127.0.0.1:8103'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mport\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;36m8203\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;31m# notebook_url=\"http://localhost:8888\"\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
+ "\u001b[0;32m/home/HPC/sterbini/py38/lib/python3.8/site-packages/bokeh/io/showing.py\u001b[0m in \u001b[0;36mshow\u001b[0;34m(obj, browser, new, notebook_handle, notebook_url, **kw)\u001b[0m\n\u001b[1;32m 135\u001b[0m \u001b[0;31m# in Tornado) just in order to show a non-server object\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 136\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mis_application\u001b[0m \u001b[0;32mor\u001b[0m \u001b[0mcallable\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mobj\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 137\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mrun_notebook_hook\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mstate\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mnotebook_type\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'app'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mobj\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mstate\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mnotebook_url\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkw\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 138\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 139\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0m_show_with_state\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mobj\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mstate\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mbrowser\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mnew\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mnotebook_handle\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mnotebook_handle\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+ "\u001b[0;32m/home/HPC/sterbini/py38/lib/python3.8/site-packages/bokeh/io/notebook.py\u001b[0m in \u001b[0;36mrun_notebook_hook\u001b[0;34m(notebook_type, action, *args, **kw)\u001b[0m\n\u001b[1;32m 296\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0m_HOOKS\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mnotebook_type\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0maction\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 297\u001b[0m \u001b[0;32mraise\u001b[0m \u001b[0mRuntimeError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"notebook hook for %r did not install %r action\"\u001b[0m \u001b[0;34m%\u001b[0m \u001b[0mnotebook_type\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0maction\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 298\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0m_HOOKS\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mnotebook_type\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0maction\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkw\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 299\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 300\u001b[0m \u001b[0;31m#-----------------------------------------------------------------------------\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+ "\u001b[0;32m/home/HPC/sterbini/py38/lib/python3.8/site-packages/bokeh/io/notebook.py\u001b[0m in \u001b[0;36mshow_app\u001b[0;34m(app, state, notebook_url, port, **kw)\u001b[0m\n\u001b[1;32m 472\u001b[0m \u001b[0morigin\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0m_origin_url\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mnotebook_url\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 473\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 474\u001b[0;31m \u001b[0mserver\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mServer\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m{\u001b[0m\u001b[0;34m\"/\"\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mapp\u001b[0m\u001b[0;34m}\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mio_loop\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mloop\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mport\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mport\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mallow_websocket_origin\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0morigin\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkw\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 475\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 476\u001b[0m \u001b[0mserver_id\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0muuid4\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mhex\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+ "\u001b[0;32m/home/HPC/sterbini/py38/lib/python3.8/site-packages/bokeh/server/server.py\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, applications, io_loop, http_server_kwargs, **kwargs)\u001b[0m\n\u001b[1;32m 393\u001b[0m \u001b[0mhttp_server_kwargs\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'ssl_options'\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mcontext\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 394\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 395\u001b[0;31m \u001b[0msockets\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_port\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mbind_sockets\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mopts\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0maddress\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mopts\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mport\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 396\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_address\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mopts\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0maddress\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 397\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
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--
GitLab