{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# The `Excel_plan()` -- batch scans using a spreadsheet\n", "\n", "Use a spreadsheet as a multi-sample batch scan tool. \n", "We'll need a spreadsheet with some things to be done \n", "and a plan that will read that spreadsheet and act on it. \n", "\n", "This plan will:\n", "\n", "* [x] use an Excel spreadsheet (for starters)\n", "* [x] read a table from the spreadsheet file\n", "* [x] take a single action from each row in the table\n", "* [x] decide action based on a specific named column in the table\n", "* [x] report all columns as metadata for the action\n", "* [x] ignore empty rows\n", "* [ ] ignore any data outside of the table boundaries\n", "\n", "Since the actions and parameters (args & kwargs) will be \n", "different in every implementation, this may prove difficult \n", "to generalize.given a spreadsheet (named ``sample_example.xlsx``)\n", "with content as shown in the next figure:\n", "\n", "![sample_example.xlsx](../resources/sample_example.jpg)\n", "\n", "**Tip**: Place the column labels on the fourth row of the spreadsheet, starting\n", "in the first column. The actions start on the next row. The first blank row\n", "indicates the end of the command table within the spreadsheet. Use as many\n", "columns as you need, one column per argument.\n", "\n", "Here's the demo, starting with the bluesky setup." ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [], "source": [ "# Import matplotlib and put it in interactive mode.\n", "%matplotlib notebook\n", "import matplotlib.pyplot as plt\n", "plt.ion()\n", "\n", "import pathlib\n", "\n", "import databroker\n", "cat = databroker.temp()\n", "\n", "from bluesky import RunEngine\n", "import bluesky.plans as bp\n", "import bluesky.plan_stubs as bps\n", "from bluesky.callbacks.best_effort import BestEffortCallback\n", "from bluesky import SupplementalData\n", "from bluesky.simulators import summarize_plan\n", "from bluesky.suspenders import SuspendFloor\n", "\n", "from ophyd.sim import motor1, motor2, motor3, SynGauss\n", "\n", "import apstools.devices as APS_devices\n", "import apstools.utils as APS_utils\n", "\n", "RE = RunEngine({})\n", "RE.subscribe(cat.v1.insert)\n", "RE.subscribe(BestEffortCallback())\n", "RE.preprocessors.append(SupplementalData())\n", "\n", "shutter = APS_devices.SimulatedApsPssShutterWithStatus(name=\"shutter\")\n", "watch_for_shutter_close = SuspendFloor(shutter.pss_state, 1)\n", "\n", "noisy_det = SynGauss('noisy_det', motor1, 'motor1', center=0, Imax=1,\n", " noise='uniform', sigma=0.9, noise_multiplier=0.1, labels={'detectors'})\n", "noisy_det.kind = \"hinted\"" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "----\n", "\n", "## Excel plan and infrastructure" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "shutter -> open\n", "motor2 -> 5.07\n", "motor3 -> 8.3\n", "Scan_Type: step_scan\n", "sx: 5.07\n", "sy: 8.3\n", "Thickness: 0\n", "Sample_Name: Water Blank\n", "remarks: deionized\n", "code_number: None\n", "table_row: 1\n", "Excel_file: sample_example.xlsx\n", "xl_file: sample_example.xlsx\n", "original_keys: {'Scan_Type': 'Scan Type', 'sx': 'sx', 'sy': 'sy', 'Thickness': 'Thickness', 'Sample_Name': 'Sample Name', 'remarks': 'remarks', 'code_number': 'code number'}\n", "motor2: 0\n", "motor3: 0\n", "shutter: close\n", "=================================== Open Run ===================================\n", "motor1 -> -5.0\n", " Read ['noisy_det', 'motor1']\n", "motor1 -> -3.571428571428571\n", " Read ['noisy_det', 'motor1']\n", "motor1 -> -2.142857142857143\n", " Read ['noisy_det', 'motor1']\n", "motor1 -> -0.7142857142857144\n", " Read ['noisy_det', 'motor1']\n", "motor1 -> 0.7142857142857144\n", " Read ['noisy_det', 'motor1']\n", "motor1 -> 2.1428571428571432\n", " Read ['noisy_det', 'motor1']\n", "motor1 -> 3.571428571428571\n", " Read ['noisy_det', 'motor1']\n", "motor1 -> 5.0\n", " Read ['noisy_det', 'motor1']\n", "================================== Close Run ===================================\n", "no handling for table row 2: OrderedDict([('Scan Type', 'other_scan'), ('sx', 5.07), ('sy', 8.3), ('Thickness', 0), ('Sample Name', 'Water Blank'), ('remarks', 'deionized'), ('code number', None)])\n", "no handling for table row 3: OrderedDict([('Scan Type', 'this will be ignored (and also the next blank row will be ignored)'), ('sx', None), ('sy', None), ('Thickness', None), ('Sample Name', None), ('remarks', None), ('code number', None)])\n", "shutter -> close\n", "motor1 -> 0\n", "motor2 -> 0\n", "motor3 -> 0\n" ] } ], "source": [ "def beforeExcelPlan():\n", " \"\"\"things to be done at the start of every Excel plan\"\"\"\n", " yield from bps.mv(\n", " shutter, \"open\", # for example\n", " )\n", "\n", " \n", "def afterExcelPlan():\n", " \"\"\"things to be done at the end of every Excel plan\"\"\"\n", " yield from bps.mv(\n", " shutter, \"close\", # for example\n", " motor1, 0, # park the motors\n", " motor2, 0,\n", " motor3, 0,\n", " )\n", "\n", "\n", "def common_step_scan(pos_X, pos_Y, thickness, scan_title, md={}):\n", " \"\"\"\n", " run a step scan over a common range at given sample position\n", " \"\"\"\n", " yield from bps.mv(\n", " motor2, pos_X,\n", " motor3, pos_Y,\n", " )\n", " md[motor2.name] = motor2.position\n", " md[motor3.name] = motor3.position\n", " md[\"shutter\"] = shutter.state\n", " for k, v in md.items():\n", " print(f\"{k}: {v}\")\n", "\n", " yield from bps.install_suspender(watch_for_shutter_close)\n", " yield from bp.scan([noisy_det], motor1, -5, 5, 8, md=md)\n", " yield from bps.remove_suspender(watch_for_shutter_close)\n", "\n", "\n", "def Excel_plan(xl_file, md={}):\n", " \"\"\"\n", " example of reading a list of samples from Excel spreadsheet\n", " \n", " USAGE::\n", " \n", " summarize_plan(run_Excel_file(\"sample_example.xlsx\"))\n", " RE(run_Excel_file(\"sample_example.xlsx\"))\n", " \"\"\"\n", " excel_file = pathlib.Path(xl_file)\n", " assert excel_file.exists()\n", " xl = APS_utils.ExcelDatabaseFileGeneric(str(excel_file))\n", "\n", " yield from beforeExcelPlan()\n", " for i, row in enumerate(xl.db.values()):\n", " # print(f\"row={row}\")\n", " \n", " # metadata\n", " # all parameters from this row go into the metadata\n", " # columns names are the keys in the metadata dictionary\n", " # make sure md keys are \"clean\"\n", " # also provide crossreference to original column names\n", " _md = {APS_utils.cleanupText(k): v for k, v in row.items()}\n", " _md[\"table_row\"] = i+1\n", " _md[\"Excel_file\"] = str(excel_file)\n", " _md[\"xl_file\"] = xl_file\n", " _md[\"original_keys\"] = {APS_utils.cleanupText(k): k for k in row.keys()}\n", " _md.update(md) # overlay with user-supplied metadata\n", "\n", " scan_command = (row[\"Scan Type\"] or \"\").lower()\n", " if scan_command == \"step_scan\":\n", " yield from common_step_scan(\n", " row[\"sx\"], # label must match cell string EXACTLY\n", " row[\"sy\"], \n", " row[\"Thickness\"], \n", " row[\"Sample Name\"],\n", " # add all input as scan metadata, ensure the keys are clean\n", " md=_md,\n", " )\n", " elif scan_command == \"some_other_action\":\n", " pass # TODO: suggestion\n", " else:\n", " print(f\"no handling for table row {i+1}: {row}\")\n", " yield from afterExcelPlan()\n", "\n", "\n", "summarize_plan(Excel_plan(\"sample_example.xlsx\"))" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Scan_Type: step_scan\n", "sx: 5.07\n", "sy: 8.3\n", "Thickness: 0\n", "Sample_Name: Water Blank\n", "remarks: deionized\n", "code_number: None\n", "table_row: 1\n", "Excel_file: sample_example.xlsx\n", "xl_file: sample_example.xlsx\n", "original_keys: {'Scan_Type': 'Scan Type', 'sx': 'sx', 'sy': 'sy', 'Thickness': 'Thickness', 'Sample_Name': 'Sample Name', 'remarks': 'remarks', 'code_number': 'code number'}\n", "motor2: 5.07\n", "motor3: 8.3\n", "shutter: open\n", "\n", "\n", "Transient Scan ID: 1 Time: 2022-07-06 00:27:29\n", "Persistent Unique Scan ID: 'a6ea8a82-aff2-4621-a197-1a3bca524e51'\n", "New stream: 'primary'\n" ] }, { "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. 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But how to set the MIME type? 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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(\"
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Start
code_number None
detectors
noisy_det
Excel_file sample_example.xlsx
hints \n", " \n", " \n", " \n", " \n", "
dimensions
[['motor1'], 'primary']
motor2 5.07
motor3 8.3
motors
motor1
num_intervals 7
num_points 8
original_keys \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
code_number code number
remarks remarks
Sample_Name Sample Name
Scan_Type Scan Type
sx sx
sy sy
Thickness Thickness
plan_args \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
args
SynAxis(prefix='', name='motor1', read_attrs=['readback', 'setpoint'], configuration_attrs=['velocity', 'acceleration'])
-5
5
detectors
SynGauss(prefix='', name='noisy_det', read_attrs=['val'], configuration_attrs=['Imax', 'center', 'sigma', 'noise', 'noise_multiplier'])
num 8
per_step None
plan_name scan
plan_pattern inner_product
plan_pattern_args \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
args
SynAxis(prefix='', name='motor1', read_attrs=['readback', 'setpoint'], configuration_attrs=['velocity', 'acceleration'])
-5
5
num 8
plan_pattern_module bluesky.plan_patterns
plan_type generator
remarks deionized
Sample_Name Water Blank
scan_id 1
Scan_Type step_scan
shutter open
sx 5.07
sy 8.3
table_row 1
Thickness 0
time a second ago (2022-07-06T00:27:29.644067)
uid a6ea8a82-aff2-4621-a197-1a3bca524e51
versions \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
bluesky 1.8.3
ophyd 1.6.4
xl_file sample_example.xlsx
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Stop
exit_status success
num_events \n", " \n", " \n", " \n", " \n", "
primary 8
reason
run_start a6ea8a82-aff2-4621-a197-1a3bca524e51
time a second ago (2022-07-06T00:27:29.781108)
uid 128c5ecf-2c21-497e-b7f1-6b74614bfb45
\n", " \n", " \n", " \n", "
Descriptors
\n", "\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
primary
configuration \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
motor1 \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
data \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
motor1_acceleration 1
motor1_velocity 1
data_keys \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
motor1_acceleration \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
dtype integer
shape
source SIM:motor1_acceleration
motor1_velocity \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
dtype integer
shape
source SIM:motor1_velocity
timestamps \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
motor1_acceleration 1657085249.0746343
motor1_velocity 1657085249.0746002
noisy_det \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
data \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
noisy_det_center 0
noisy_det_Imax 1
noisy_det_noise uniform
noisy_det_noise_multiplier 0.1
noisy_det_sigma 0.9
data_keys \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
noisy_det_center \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
dtype integer
shape
source SIM:noisy_det_center
noisy_det_Imax \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
dtype integer
shape
source SIM:noisy_det_Imax
noisy_det_noise \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
dtype integer
enum_strs
none
poisson
uniform
shape
source SIM:noisy_det_noise
noisy_det_noise_multiplier \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
dtype number
shape
source SIM:noisy_det_noise_multiplier
noisy_det_sigma \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
dtype number
shape
source SIM:noisy_det_sigma
timestamps \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
noisy_det_center 1657085249.298179
noisy_det_Imax 1657085249.2981858
noisy_det_noise 1657085249.298202
noisy_det_noise_multiplier 1657085249.2982059
noisy_det_sigma 1657085249.2981968
data_keys \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
motor1 \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
dtype number
object_name motor1
precision 3
shape
source SIM:motor1
motor1_setpoint \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
dtype number
object_name motor1
precision 3
shape
source SIM:motor1_setpoint
noisy_det \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
dtype number
object_name noisy_det
precision 3
shape
source SIM:noisy_det
hints \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
motor1 \n", " \n", " \n", " \n", " \n", "
fields
motor1
noisy_det \n", " \n", " \n", " \n", " \n", "
fields
noisy_det
name primary
object_keys \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
motor1
motor1
motor1_setpoint
noisy_det
noisy_det
run_start a6ea8a82-aff2-4621-a197-1a3bca524e51
time a second ago (2022-07-06T00:27:29.654973)
uid 9fc2e538-dfde-48a0-a70a-b6ad3ac3c493
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