{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# 3D Flex: Custom Latent Trajectory\n", "\n", "```{note}\n", "[Read the tutorial](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/tutorial-3d-flexible-refinement) to learn more about 3D Flexible Refinement.\n", "```\n", "\n", "This example covers the following:\n", "\n", "* Load particle latent coordinates from a 3D Flex Training job\n", "* Plot the latent coordinates\n", "* Interactively draw a trajectory through the latent space\n", "* Output the trajectory as a new output in CryoSPARC\n", "\n", "The resulting trajectory may be used as input to the 3D Flex Generator job to generate a volume series along the trajectory. In this way, you can visualize specific regions or pathways through the latent conformational distribution of the particle." ] }, { "cell_type": "code", "execution_count": 1, "metadata": { "vscode": { "languageId": "python" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Connection succeeded to CryoSPARC command_core at http://cryoem5:40002\n", "Connection succeeded to CryoSPARC command_vis at http://cryoem5:40003\n" ] } ], "source": [ "import numpy as n\n", "from cryosparc.tools import CryoSPARC\n", "\n", "cs = CryoSPARC(host=\"cryoem5\", base_port=40000)\n", "assert cs.test_connection()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Load the particles dataset from the 3D Flex Training job." ] }, { "cell_type": "code", "execution_count": 9, "metadata": { "vscode": { "languageId": "python" } }, "outputs": [ { "data": { "text/html": [ "
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" ], "text/plain": [ " components_mode_0/component components_mode_0/value \\\n", "0 0 0.016000 \n", "1 0 -0.122667 \n", "2 0 -0.496000 \n", "3 0 0.357333 \n", "4 0 0.698667 \n", "... ... ... \n", "83995 0 0.229333 \n", "83996 0 -0.208000 \n", "83997 0 0.069333 \n", "83998 0 -0.176000 \n", "83999 0 0.890667 \n", "\n", " components_mode_1/component components_mode_1/value \\\n", "0 1 0.314667 \n", "1 1 -0.293333 \n", "2 1 0.048000 \n", "3 1 0.133333 \n", "4 1 0.048000 \n", "... ... ... \n", "83995 1 0.314667 \n", "83996 1 0.784000 \n", "83997 1 0.005333 \n", "83998 1 0.272000 \n", "83999 1 0.048000 \n", "\n", " uid \n", "0 3070975014664207456 \n", "1 4618435520677801850 \n", "2 5473205460946538064 \n", "3 16310523440862460071 \n", "4 13340786341065263892 \n", "... ... \n", "83995 16055293458929423443 \n", "83996 4138809144408497890 \n", "83997 12856011472364466207 \n", "83998 14511870028664140377 \n", "83999 17110459322516273008 \n", "\n", "[84000 rows x 5 columns]" ] }, "execution_count": 9, "metadata": {}, "output_type": "execute_result" } ], "source": [ "import pandas as pd\n", "\n", "project = cs.find_project(\"P251\")\n", "particles = project.find_job(\"J21\").load_output(\"particles\")\n", "\n", "pd.DataFrame(particles.rows())" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Create an interative plot that responds to on-click events. \n", "\n", "Once the plot is drawn, click repeatedly on the plot along a trajectory you wish to sample in the latent space. The points along this trajectory will form the output of the notebook and be used in 3D Flex Generator." ] }, { "cell_type": "code", "execution_count": 6, "metadata": { "vscode": { "languageId": "python" } }, "outputs": [ { "data": { "application/javascript": "/* Put everything inside the global mpl namespace */\n/* global mpl */\nwindow.mpl = {};\n\nmpl.get_websocket_type = function () {\n if (typeof WebSocket !== 'undefined') {\n return WebSocket;\n } else if (typeof MozWebSocket !== 'undefined') {\n return MozWebSocket;\n } else {\n alert(\n 'Your browser does not have WebSocket support. ' +\n 'Please try Chrome, Safari or Firefox ≥ 6. ' +\n 'Firefox 4 and 5 are also supported but you ' +\n 'have to enable WebSockets in about:config.'\n );\n }\n};\n\nmpl.figure = function (figure_id, websocket, ondownload, parent_element) {\n this.id = figure_id;\n\n this.ws = websocket;\n\n this.supports_binary = this.ws.binaryType !== undefined;\n\n if (!this.supports_binary) {\n var warnings = document.getElementById('mpl-warnings');\n if (warnings) {\n warnings.style.display = 'block';\n warnings.textContent =\n 'This browser does not support binary websocket messages. 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But how to set the MIME type? It doesn't seem\n * to be part of the websocket stream */\n img.type = 'image/png';\n }\n\n /* Free the memory for the previous frames */\n if (fig.imageObj.src) {\n (window.URL || window.webkitURL).revokeObjectURL(\n fig.imageObj.src\n );\n }\n\n fig.imageObj.src = (window.URL || window.webkitURL).createObjectURL(\n img\n );\n fig.updated_canvas_event();\n fig.waiting = false;\n return;\n } else if (\n typeof evt.data === 'string' &&\n evt.data.slice(0, 21) === 'data:image/png;base64'\n ) {\n fig.imageObj.src = evt.data;\n fig.updated_canvas_event();\n fig.waiting = false;\n return;\n }\n\n var msg = JSON.parse(evt.data);\n var msg_type = msg['type'];\n\n // Call the \"handle_{type}\" callback, which takes\n // the figure and JSON message as its only arguments.\n try {\n var callback = fig['handle_' + msg_type];\n } catch (e) {\n console.log(\n \"No handler for the '\" + msg_type + \"' message type: \",\n msg\n );\n return;\n }\n\n if (callback) {\n try {\n // console.log(\"Handling '\" + msg_type + \"' message: \", msg);\n callback(fig, msg);\n } catch (e) {\n console.log(\n \"Exception inside the 'handler_\" + msg_type + \"' callback:\",\n e,\n e.stack,\n msg\n );\n }\n }\n };\n};\n\n// from https://stackoverflow.com/questions/1114465/getting-mouse-location-in-canvas\nmpl.findpos = function (e) {\n //this section is from http://www.quirksmode.org/js/events_properties.html\n var targ;\n if (!e) {\n e = window.event;\n }\n if (e.target) {\n targ = e.target;\n } else if (e.srcElement) {\n targ = e.srcElement;\n }\n if (targ.nodeType === 3) {\n // defeat Safari bug\n targ = targ.parentNode;\n }\n\n // pageX,Y are the mouse positions relative to the document\n var boundingRect = targ.getBoundingClientRect();\n var x = e.pageX - (boundingRect.left + document.body.scrollLeft);\n var y = e.pageY - (boundingRect.top + document.body.scrollTop);\n\n return { x: x, y: y };\n};\n\n/*\n * return a copy of an object with only non-object keys\n * we need this to avoid circular references\n * https://stackoverflow.com/a/24161582/3208463\n */\nfunction simpleKeys(original) {\n return Object.keys(original).reduce(function (obj, key) {\n if (typeof original[key] !== 'object') {\n obj[key] = original[key];\n }\n return obj;\n }, {});\n}\n\nmpl.figure.prototype.mouse_event = function (event, name) {\n var canvas_pos = mpl.findpos(event);\n\n if (name === 'button_press') {\n this.canvas.focus();\n this.canvas_div.focus();\n }\n\n var x = canvas_pos.x * this.ratio;\n var y = canvas_pos.y * this.ratio;\n\n this.send_message(name, {\n x: x,\n y: y,\n button: event.button,\n step: event.step,\n guiEvent: simpleKeys(event),\n });\n\n /* This prevents the web browser from automatically changing to\n * the text insertion cursor when the button is pressed. We want\n * to control all of the cursor setting manually through the\n * 'cursor' event from matplotlib */\n event.preventDefault();\n return false;\n};\n\nmpl.figure.prototype._key_event_extra = function (_event, _name) {\n // Handle any extra behaviour associated with a key event\n};\n\nmpl.figure.prototype.key_event = function (event, name) {\n // Prevent repeat events\n if (name === 'key_press') {\n if (event.key === this._key) {\n return;\n } else {\n this._key = event.key;\n }\n }\n if (name === 'key_release') {\n this._key = null;\n }\n\n var value = '';\n if (event.ctrlKey && event.key !== 'Control') {\n value += 'ctrl+';\n }\n else if (event.altKey && event.key !== 'Alt') {\n value += 'alt+';\n }\n else if (event.shiftKey && event.key !== 'Shift') {\n value += 'shift+';\n }\n\n value += 'k' + event.key;\n\n this._key_event_extra(event, name);\n\n this.send_message(name, { key: value, guiEvent: simpleKeys(event) });\n return false;\n};\n\nmpl.figure.prototype.toolbar_button_onclick = function (name) {\n if (name === 'download') {\n this.handle_save(this, null);\n } else {\n this.send_message('toolbar_button', { name: name });\n }\n};\n\nmpl.figure.prototype.toolbar_button_onmouseover = function (tooltip) {\n this.message.textContent = tooltip;\n};\n\n///////////////// REMAINING CONTENT GENERATED BY embed_js.py /////////////////\n// prettier-ignore\nvar _JSXTOOLS_RESIZE_OBSERVER=function(A){var t,i=new WeakMap,n=new WeakMap,a=new WeakMap,r=new WeakMap,o=new Set;function s(e){if(!(this instanceof s))throw new TypeError(\"Constructor requires 'new' operator\");i.set(this,e)}function h(){throw new TypeError(\"Function is not a constructor\")}function c(e,t,i,n){e=0 in arguments?Number(arguments[0]):0,t=1 in arguments?Number(arguments[1]):0,i=2 in arguments?Number(arguments[2]):0,n=3 in arguments?Number(arguments[3]):0,this.right=(this.x=this.left=e)+(this.width=i),this.bottom=(this.y=this.top=t)+(this.height=n),Object.freeze(this)}function d(){t=requestAnimationFrame(d);var s=new WeakMap,p=new Set;o.forEach((function(t){r.get(t).forEach((function(i){var r=t instanceof window.SVGElement,o=a.get(t),d=r?0:parseFloat(o.paddingTop),f=r?0:parseFloat(o.paddingRight),l=r?0:parseFloat(o.paddingBottom),u=r?0:parseFloat(o.paddingLeft),g=r?0:parseFloat(o.borderTopWidth),m=r?0:parseFloat(o.borderRightWidth),w=r?0:parseFloat(o.borderBottomWidth),b=u+f,F=d+l,v=(r?0:parseFloat(o.borderLeftWidth))+m,W=g+w,y=r?0:t.offsetHeight-W-t.clientHeight,E=r?0:t.offsetWidth-v-t.clientWidth,R=b+v,z=F+W,M=r?t.width:parseFloat(o.width)-R-E,O=r?t.height:parseFloat(o.height)-z-y;if(n.has(t)){var k=n.get(t);if(k[0]===M&&k[1]===O)return}n.set(t,[M,O]);var S=Object.create(h.prototype);S.target=t,S.contentRect=new c(u,d,M,O),s.has(i)||(s.set(i,[]),p.add(i)),s.get(i).push(S)}))})),p.forEach((function(e){i.get(e).call(e,s.get(e),e)}))}return s.prototype.observe=function(i){if(i instanceof window.Element){r.has(i)||(r.set(i,new Set),o.add(i),a.set(i,window.getComputedStyle(i)));var n=r.get(i);n.has(this)||n.add(this),cancelAnimationFrame(t),t=requestAnimationFrame(d)}},s.prototype.unobserve=function(i){if(i instanceof window.Element&&r.has(i)){var n=r.get(i);n.has(this)&&(n.delete(this),n.size||(r.delete(i),o.delete(i))),n.size||r.delete(i),o.size||cancelAnimationFrame(t)}},A.DOMRectReadOnly=c,A.ResizeObserver=s,A.ResizeObserverEntry=h,A}; // eslint-disable-line\nmpl.toolbar_items = [[\"Home\", \"Reset original view\", \"fa fa-home icon-home\", \"home\"], [\"Back\", \"Back to previous view\", \"fa fa-arrow-left icon-arrow-left\", \"back\"], [\"Forward\", \"Forward to next view\", \"fa fa-arrow-right icon-arrow-right\", \"forward\"], [\"\", \"\", \"\", \"\"], [\"Pan\", \"Left button pans, Right button zooms\\nx/y fixes axis, CTRL fixes aspect\", \"fa fa-arrows icon-move\", \"pan\"], [\"Zoom\", \"Zoom to rectangle\\nx/y fixes axis\", \"fa fa-square-o icon-check-empty\", \"zoom\"], [\"\", \"\", \"\", \"\"], [\"Download\", \"Download plot\", \"fa fa-floppy-o icon-save\", \"download\"]];\n\nmpl.extensions = [\"eps\", \"jpeg\", \"pgf\", \"pdf\", \"png\", \"ps\", \"raw\", \"svg\", \"tif\"];\n\nmpl.default_extension = \"png\";/* global mpl */\n\nvar comm_websocket_adapter = function (comm) {\n // Create a \"websocket\"-like object which calls the given IPython comm\n // object with the appropriate methods. Currently this is a non binary\n // socket, so there is still some room for performance tuning.\n var ws = {};\n\n ws.binaryType = comm.kernel.ws.binaryType;\n ws.readyState = comm.kernel.ws.readyState;\n function updateReadyState(_event) {\n if (comm.kernel.ws) {\n ws.readyState = comm.kernel.ws.readyState;\n } else {\n ws.readyState = 3; // Closed state.\n }\n }\n comm.kernel.ws.addEventListener('open', updateReadyState);\n comm.kernel.ws.addEventListener('close', updateReadyState);\n comm.kernel.ws.addEventListener('error', updateReadyState);\n\n ws.close = function () {\n comm.close();\n };\n ws.send = function (m) {\n //console.log('sending', m);\n comm.send(m);\n };\n // Register the callback with on_msg.\n comm.on_msg(function (msg) {\n //console.log('receiving', msg['content']['data'], msg);\n var data = msg['content']['data'];\n if (data['blob'] !== undefined) {\n data = {\n data: new Blob(msg['buffers'], { type: data['blob'] }),\n };\n }\n // Pass the mpl event to the overridden (by mpl) onmessage function.\n ws.onmessage(data);\n });\n return ws;\n};\n\nmpl.mpl_figure_comm = function (comm, msg) {\n // This is the function which gets called when the mpl process\n // starts-up an IPython Comm through the \"matplotlib\" channel.\n\n var id = msg.content.data.id;\n // Get hold of the div created by the display call when the Comm\n // socket was opened in Python.\n var element = document.getElementById(id);\n var ws_proxy = comm_websocket_adapter(comm);\n\n function ondownload(figure, _format) {\n window.open(figure.canvas.toDataURL());\n }\n\n var fig = new mpl.figure(id, ws_proxy, ondownload, element);\n\n // Call onopen now - mpl needs it, as it is assuming we've passed it a real\n // web socket which is closed, not our websocket->open comm proxy.\n ws_proxy.onopen();\n\n fig.parent_element = element;\n fig.cell_info = mpl.find_output_cell(\"
\");\n if (!fig.cell_info) {\n console.error('Failed to find cell for figure', id, fig);\n return;\n }\n fig.cell_info[0].output_area.element.on(\n 'cleared',\n { fig: fig },\n fig._remove_fig_handler\n );\n};\n\nmpl.figure.prototype.handle_close = function (fig, msg) {\n var width = fig.canvas.width / fig.ratio;\n fig.cell_info[0].output_area.element.off(\n 'cleared',\n fig._remove_fig_handler\n );\n fig.resizeObserverInstance.unobserve(fig.canvas_div);\n\n // Update the output cell to use the data from the current canvas.\n fig.push_to_output();\n var dataURL = fig.canvas.toDataURL();\n // Re-enable the keyboard manager in IPython - without this line, in FF,\n // the notebook keyboard shortcuts fail.\n IPython.keyboard_manager.enable();\n fig.parent_element.innerHTML =\n '';\n fig.close_ws(fig, msg);\n};\n\nmpl.figure.prototype.close_ws = function (fig, msg) {\n fig.send_message('closing', msg);\n // fig.ws.close()\n};\n\nmpl.figure.prototype.push_to_output = function (_remove_interactive) {\n // Turn the data on the canvas into data in the output cell.\n var width = this.canvas.width / this.ratio;\n var dataURL = this.canvas.toDataURL();\n this.cell_info[1]['text/html'] =\n '';\n};\n\nmpl.figure.prototype.updated_canvas_event = function () {\n // Tell IPython that the notebook contents must change.\n IPython.notebook.set_dirty(true);\n this.send_message('ack', {});\n var fig = this;\n // Wait a second, then push the new image to the DOM so\n // that it is saved nicely (might be nice to debounce this).\n setTimeout(function () {\n fig.push_to_output();\n }, 1000);\n};\n\nmpl.figure.prototype._init_toolbar = function () {\n var fig = this;\n\n var toolbar = document.createElement('div');\n toolbar.classList = 'btn-toolbar';\n this.root.appendChild(toolbar);\n\n function on_click_closure(name) {\n return function (_event) {\n return fig.toolbar_button_onclick(name);\n };\n }\n\n function on_mouseover_closure(tooltip) {\n return function (event) {\n if (!event.currentTarget.disabled) {\n return fig.toolbar_button_onmouseover(tooltip);\n }\n };\n }\n\n fig.buttons = {};\n var buttonGroup = document.createElement('div');\n buttonGroup.classList = 'btn-group';\n var button;\n for (var toolbar_ind in mpl.toolbar_items) {\n var name = mpl.toolbar_items[toolbar_ind][0];\n var tooltip = mpl.toolbar_items[toolbar_ind][1];\n var image = mpl.toolbar_items[toolbar_ind][2];\n var method_name = mpl.toolbar_items[toolbar_ind][3];\n\n if (!name) {\n /* Instead of a spacer, we start a new button group. */\n if (buttonGroup.hasChildNodes()) {\n toolbar.appendChild(buttonGroup);\n }\n buttonGroup = document.createElement('div');\n buttonGroup.classList = 'btn-group';\n continue;\n }\n\n button = fig.buttons[name] = document.createElement('button');\n button.classList = 'btn btn-default';\n button.href = '#';\n button.title = name;\n button.innerHTML = '';\n button.addEventListener('click', on_click_closure(method_name));\n button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n buttonGroup.appendChild(button);\n }\n\n if (buttonGroup.hasChildNodes()) {\n toolbar.appendChild(buttonGroup);\n }\n\n // Add the status bar.\n var status_bar = document.createElement('span');\n status_bar.classList = 'mpl-message pull-right';\n toolbar.appendChild(status_bar);\n this.message = status_bar;\n\n // Add the close button to the window.\n var buttongrp = document.createElement('div');\n buttongrp.classList = 'btn-group inline pull-right';\n button = document.createElement('button');\n button.classList = 'btn btn-mini btn-primary';\n button.href = '#';\n button.title = 'Stop Interaction';\n button.innerHTML = '';\n button.addEventListener('click', function (_evt) {\n fig.handle_close(fig, {});\n });\n button.addEventListener(\n 'mouseover',\n on_mouseover_closure('Stop Interaction')\n );\n buttongrp.appendChild(button);\n var titlebar = this.root.querySelector('.ui-dialog-titlebar');\n titlebar.insertBefore(buttongrp, titlebar.firstChild);\n};\n\nmpl.figure.prototype._remove_fig_handler = function (event) {\n var fig = event.data.fig;\n if (event.target !== this) {\n // Ignore bubbled events from children.\n return;\n }\n fig.close_ws(fig, {});\n};\n\nmpl.figure.prototype._root_extra_style = function (el) {\n el.style.boxSizing = 'content-box'; // override notebook setting of border-box.\n};\n\nmpl.figure.prototype._canvas_extra_style = function (el) {\n // this is important to make the div 'focusable\n el.setAttribute('tabindex', 0);\n // reach out to IPython and tell the keyboard manager to turn it's self\n // off when our div gets focus\n\n // location in version 3\n if (IPython.notebook.keyboard_manager) {\n IPython.notebook.keyboard_manager.register_events(el);\n } else {\n // location in version 2\n IPython.keyboard_manager.register_events(el);\n }\n};\n\nmpl.figure.prototype._key_event_extra = function (event, _name) {\n // Check for shift+enter\n if (event.shiftKey && event.which === 13) {\n this.canvas_div.blur();\n // select the cell after this one\n var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n IPython.notebook.select(index + 1);\n }\n};\n\nmpl.figure.prototype.handle_save = function (fig, _msg) {\n fig.ondownload(fig, null);\n};\n\nmpl.find_output_cell = function (html_output) {\n // Return the cell and output element which can be found *uniquely* in the notebook.\n // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n // IPython event is triggered only after the cells have been serialised, which for\n // our purposes (turning an active figure into a static one), is too late.\n var cells = IPython.notebook.get_cells();\n var ncells = cells.length;\n for (var i = 0; i < ncells; i++) {\n var cell = cells[i];\n if (cell.cell_type === 'code') {\n for (var j = 0; j < cell.output_area.outputs.length; j++) {\n var data = cell.output_area.outputs[j];\n if (data.data) {\n // IPython >= 3 moved mimebundle to data attribute of output\n data = data.data;\n }\n if (data['text/html'] === html_output) {\n return [cell, data, j];\n }\n }\n }\n }\n};\n\n// Register the function which deals with the matplotlib target/channel.\n// The kernel may be null if the page has been refreshed.\nif (IPython.notebook.kernel !== null) {\n IPython.notebook.kernel.comm_manager.register_target(\n 'matplotlib',\n mpl.mpl_figure_comm\n );\n}\n", "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "from matplotlib import pyplot as plt\n", "\n", "fig = plt.figure(figsize=(5, 5))\n", "\n", "\n", "def do_plot():\n", " plt.plot(\n", " particles[\"components_mode_0/value\"][::10],\n", " particles[\"components_mode_1/value\"][::10],\n", " \".\",\n", " alpha=0.5,\n", " color=\"gray\",\n", " )\n", " plt.grid()\n", "\n", "\n", "do_plot()\n", "\n", "chain = True\n", "pts = []\n", "\n", "\n", "def onclick(event):\n", " fig.clf()\n", " do_plot()\n", " pts.append([event.xdata, event.ydata])\n", " apts = n.array(pts)\n", " if chain:\n", " plt.plot(apts[0, 0], apts[0, 1], \"xk\")\n", " plt.plot(apts[:, 0], apts[:, 1], \".-r\")\n", " else:\n", " for k, i in enumerate(range(0, len(apts), 2)):\n", " plt.plot(apts[i, 0], apts[i, 1], \"xk\")\n", " plt.plot(apts[i : i + 2, 0], apts[i : i + 2, 1], \".-\", label=str(k))\n", " plt.legend()\n", "\n", "\n", "cid = plt.gcf().canvas.mpl_connect(\"button_press_event\", onclick)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Print out the selected trajectory points." ] }, { "cell_type": "code", "execution_count": 7, "metadata": { "vscode": { "languageId": "python" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 0.05, -0.52\n", "-0.13, -0.47\n", "-0.26, -0.32\n", "-0.34, -0.14\n", "-0.35, -0.06\n", "-0.35, 0.08\n", "-0.35, 0.18\n", "-0.28, 0.23\n", "-0.16, 0.27\n", "-0.06, 0.27\n", " 0.00, 0.27\n", " 0.23, 0.27\n", " 0.25, 0.31\n", " 0.25, 0.40\n", " 0.21, 0.45\n", " 0.16, 0.46\n", " 0.06, 0.49\n", "-0.07, 0.51\n", "-0.20, 0.49\n", "-0.34, 0.37\n", "-0.47, 0.28\n", "-0.52, -0.00\n", "-0.50, -0.20\n", "-0.45, -0.26\n", "-0.26, -0.27\n", "-0.23, -0.27\n", "-0.07, -0.30\n", " 0.19, -0.32\n", " 0.26, -0.26\n", " 0.29, -0.20\n", " 0.29, -0.20\n", " 0.29, -0.20\n", " 0.30, -0.11\n", " 0.38, -0.07\n", " 0.50, -0.04\n", " 0.56, 0.05\n", " 0.56, 0.06\n", " 0.56, 0.06\n" ] } ], "source": [ "latent_pts = n.array(pts)\n", "for pt in latent_pts:\n", " print(f\"{pt[0]:5.2f}, {pt[1]:5.2f}\")" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Set up an external job to save the custom latent components. Connect to the train job to ensure output fields get passed through." ] }, { "cell_type": "code", "execution_count": 11, "metadata": { "vscode": { "languageId": "python" } }, "outputs": [], "source": [ "job = project.create_external_job(\"W4\", \"Custom Latents\")\n", "job.connect(\"particles\", \"J21\", \"particles\", slots=[\"components_mode_%d\" % k for k in range(2)])" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Add and allocate an output for the job to store the custom latent components." ] }, { "cell_type": "code", "execution_count": 22, "metadata": { "vscode": { "languageId": "python" } }, "outputs": [], "source": [ "latents_dset = job.add_output(\n", " type=\"particle\",\n", " name=\"latents\",\n", " slots=[{\"prefix\": \"components_mode_%d\" % k, \"dtype\": \"components\", \"required\": True} for k in range(2)],\n", " title=\"Latents\",\n", " alloc=len(latent_pts),\n", ")" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Save the points into the allocated dataset." ] }, { "cell_type": "code", "execution_count": 23, "metadata": { "vscode": { "languageId": "python" } }, "outputs": [], "source": [ "for k in range(2):\n", " latents_dset[\"components_mode_%d/component\" % k] = k\n", " latents_dset[\"components_mode_%d/value\" % k] = latent_pts[:, k]" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Save the output." ] }, { "cell_type": "code", "execution_count": 24, "metadata": { "vscode": { "languageId": "python" } }, "outputs": [], "source": [ "with job.run():\n", " job.save_output(\"latents\", latents_dset)" ] } ], "metadata": { "anaconda-cloud": {}, "kernelspec": { "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" } }, "nbformat": 4, "nbformat_minor": 1 }