IOPub limit reached

[bdigirolamo]

Hello,

Great app. I have an issue on my iPad as follows:

IOPub data rate exceeded.
….
To change this limit, set the config variable
—ServerApp.iopub_data_rate_limit

Current values:
ServerApp.iopub_data_rate_limit = 1000000.0 (bytes/sec)
ServerApp.rate_limit_window=3.0s (secs)

How can I set this variable?
thanks

[holzschu]

Hi,
with a data rate limit at one million bytes per second, I think that the issue is not the data rate itself (i.e. I'm skeptical of the error message). Can you provide me with the notebook or a way to reproduce the error?

[bdigirolamo]

HelloThanks for the prompt answer. Could it be also related to my hardware? I have a 2020 iPad 256 GB. Here you find the notebook while for the data you can download it at: https://cernbox.cern.ch/s/sCMJL2bcuBL7m0nThe notebook is not complete with the plotting part, but that’s not an issueThanks for your helpBeniaminoSent from my iPadOn 5 Jun 2024, at 11:49, Nicolas Holzschuch ***@***.***> wrote: Hi, with a data rate limit at one million bytes per second, I think that the issue is not the data rate itself (i.e. I'm skeptical of the error message). Can you provide me with the notebook or a way to reproduce the error? —Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you authored the thread.Message ID: ***@***.***>

[holzschu]

I'm afraid the notebook does not appear here (github removes the pieces attached to e-mail) and I cannot download the data using the link provided either.

[bdigirolamo]

All right. I paste here the code (I couldn’t export it other than cryptical LaTeX, so I opened in emacs. I add down also few lines of the data file that has the following name: PLI01_2024.06.04-RAW.txt I would have liked to pass you the full file because it is a 2582546 lines file, but if you can’t download I could do better. Thanks Beniamino —————Start of code————— { "cells": [ { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [], "source": [ "import os\n", "import sys" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [], "source": [ "import matplotlib.pyplot as plt\n", "import matplotlib.gridspec as gridspec\n", "import matplotlib.dates as mdates" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [], "source": [ "import time\n", "import datetime,pytz\n", "import calendar\n", "from datetime import datetime\n", "\n", "import numpy as np\n", "import scipy.signal\n", "\n", "import scipy.fftpack as fftpack\n", "# import pywt\n" ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [], "source": [ "# matrix initialise\n", "global date\n", "global xutc\n", "global secos\n", "global inc1\n", "global inc2\n", "global ref1\n", "global ref2\n", "global ertimesec\n", "date = []\n", "secos = []\n", "inc1 = []\n", "inc2 = []\n", "ref1 = []\n", "ref2 = []\n", "xutc=[]\n", "ertimesec =[]" ] }, { "cell_type": "code", "execution_count": 5, "metadata": {}, "outputs": [], "source": [ "data = \"2024.06.04\"\n", "#b = filepli.split(\"-\")\n", "c = data.split(\".\")\n", "dateq = c[0] + \"-\" + c[1] + \"-\" + c[2]\n", "#print(dateq)\n", "\n", "pli = \"PLI01\"\n", "\n", "k1 = 350\n", "k2 = 426\n", "\n", "h1 = \"00:00:00.000\"\n", "# h1 = \"02:20:00.000\"\n", "h2 = \"02:00:00.000\"\n", "#h2 = \"23:59:59.999\" \n", "#fftflag = \"fft\"\n", "# fftflag = \"no\"\n", "\n", "t1 = dateq + \" \" + h1\n", "t2 = dateq + \" \" + h2\n", "\n", "d = data\n" ] }, { "cell_type": "code", "execution_count": 6, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "accessing file PLI01_2024.06.04-RAW.txt\n" ] } ], "source": [ "filepli = pli + \"_\" + data + \"-RAW.txt\"\n", "print(\"accessing file \", filepli)" ] }, { "cell_type": "code", "execution_count": 7, "metadata": {}, "outputs": [], "source": [ "if (pli==\"PLI01\" or pli==\"PLI02\" or pli==\"PLI04\" or pli==\"PLI03\" or pli==\"PLI06\" or pli==\"PLI07\"):\n", " with open(filepli,\"r\") as quake:\n", " data = quake.readlines()[:-1]\n", " quake.close()\n", " for i, linea in enumerate(data):\n", " column = linea.split(' ')\n", " seco = float(column[1][:-3])\n", " millis = float(column[1][len(column[1])-3:])/1000.\n", " secop = seco + millis\n", " secos.append(secop)\n", " xutc.append(secop)\n", " wl1 = float(column[2])\n", " wl2 = float(column[3])\n", " wl3 = float(column[4])\n", " wl4 = float(column[5])\n", " rp1 = float(column[6])\n", " rp2 = float(column[7])\n", " rp3 = float(column[8])\n", " rp4 = float(column[9].rstrip(\"\\n\"))\n", " if (column[5] != 'NaN'):\n", " inc2cont = float(k2)*((wl1+wl4-wl2-wl3)-(rp1+rp4-rp2-rp3))\n", " ref2cont = float(k2)*(rp1+rp4-rp2-rp3)\n", " inc2.append(inc2cont)\n", " ref2.append(ref2cont)\n", " else:\n", " inc2.append(0)\n", " ref2.append(0)\n", " \n", " if (column[9] != 'NaN'):\n", " inc1cont = float(k1)*((wl3+wl4-wl1-wl2)-(rp3+rp4-rp1-rp2))\n", " ref1cont = float(k1)*(rp3+rp4-rp1-rp2)\n", " inc1.append(inc1cont)\n", " ref1.append(ref1cont)\n", " else:\n", " inc1.append(0)\n", " ref1.append(0)" ] }, { "cell_type": "code", "execution_count": 8, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "max Inc1 signal 14.281050000000004\n", "max Inc2 signal 42.921554598\n" ] } ], "source": [ "if (len(inc1)>0):\n", " meaninc1 = np.mean(inc1)\n", " print(\"max Inc1 signal\",np.max(np.absolute(inc1)))\n", "else:\n", " meaninc1 = 0\n", "\n", " \n", "if (len(inc2)>0):\n", " meaninc2 = np.mean(inc2)\n", " print(\"max Inc2 signal\",np.max(np.absolute(inc2)))\n", "else:\n", " meaninc2 = 0\n", "\n", "\n", "\n", " \n", "minc1=inc1-meaninc1\n", "minc2=inc2-meaninc2\n", "\n", "set1 = {'Inc1':(xutc,minc1),'Inc2':(xutc,minc2),'Ref1':(xutc,ref1),'Ref2':(xutc,ref2)}" ] }, { "cell_type": "code", "execution_count": 9, "metadata": {}, "outputs": [], "source": [ "# function definitions\n", "\n", "# def dwt_filter(signal, thresh = 0.3, wavelet=\"db5\"):\n", "# thresh = thresh*np.nanmax(signal)\n", "\n", "# coeff = pywt.wavedec(signal, wavelet, level=10)\n", "# coeff[1:] = (pywt.threshold(i, value=thresh, mode=\"soft\" ) for i in coeff[1:])\n", " \n", "# reconstructed_signal = pywt.waverec(coeff, wavelet)\n", "# # return reconstructed_signal\n", "# # dwt always produces an output list of even size. It may have to be truncated by one to \n", "# # match legnth of initial signal list\n", "# return reconstructed_signal[:-1] if len(signal) % 2 else reconstructed_signal\n", "\n", "\n", "def butter_bandpass(lowcut, highcut, fs, order=4):\n", " nyq = 0.5 * fs\n", " low = lowcut / nyq\n", " high = highcut / nyq\n", " sos = scipy.signal.butter(order, [low, high], btype='bandpass', output='sos')\n", " return sos\n", "\n", "\n", "def butter_bandpass_filter(data, lowcut, highcut, fs, new_order=10):\n", " sos = butter_bandpass(lowcut, highcut, fs, order = new_order)\n", " y = scipy.signal.sosfilt(sos, data)\n", " return y\n", "\n", "\n", "\n", "def move_figure(position=\"top-right\"):\n", " '''\n", " Move and resize a window to a set of standard positions on the screen.\n", " Possible positions are:\n", " top, bottom, left, right, top-left, top-right, bottom-left, bottom-right\n", " '''\n", "\n", " mgr = plt.get_current_fig_manager()\n", " #mgr.full_screen_toggle() # primitive but works to get screen size\n", " py = 2*mgr.canvas.height()\n", " px = 2*mgr.canvas.width()\n", " print(px,py)\n", "\n", " d = 10 # width of the window border in pixels\n", " if position == \"top\":\n", " # x-top-left-corner, y-top-left-corner, x-width, y-width (in pixels)\n", " mgr.window.setGeometry(d, 4*d, px - 2*d, py/2 - 4*d)\n", " elif position == \"bottom\":\n", " mgr.window.setGeometry(d, py/2 + 5*d, px - 2*d, py/2 - 4*d)\n", " elif position == \"left\":\n", " mgr.window.setGeometry(d, 4*d, px/2 - 2*d, py - 4*d)\n", " elif position == \"right\":\n", " mgr.window.setGeometry(px/2 + d, 4*d, px/2 - 2*d, py - 4*d)\n", " elif position == \"top-left\":\n", " mgr.window.setGeometry(d, 4*d, px/2 - 2*d, py/2 - 4*d)\n", " elif position == \"top-right\":\n", " mgr.window.setGeometry(px/2 + d, 4*d, px/2 - 2*d, py/2 - 4*d)\n", " elif position == \"bottom-left\":\n", " mgr.window.setGeometry(d, py/2 + 5*d, px/2 - 2*d, py/2 - 4*d)\n", " elif position == \"bottom-right\":\n", " mgr.window.setGeometry(px/2 + d, py/2 + 5*d, px/2 - 2*d, py/2 - 4*d)\n", " \n" ] }, { "cell_type": "code", "execution_count": 10, "metadata": {}, "outputs": [], "source": [ "def fillvarpli(pli,ta,tb):\n", " print(\"processing...\")\n", " print(\"between \", ta, \" and \", tb)\n", "\n", " #year = t1.split(\"-\")\n", "\n", " ## UTC time\n", " dtobj1= datetime.strptime(ta, \"%Y-%m-%d %H:%M:%S.%f\")\n", " dtobj2= datetime.strptime(tb, \"%Y-%m-%d %H:%M:%S.%f\")\n", "\n", " dtobj11=dtobj1.replace(tzinfo=pytz.UTC) #replace method\n", " dtobj22=dtobj2.replace(tzinfo=pytz.UTC) #replace method\n", "\n", " # Convert to local time to fetch from TIMBER\n", " dtobj_1=dtobj11.astimezone(pytz.timezone(\"Europe/Vienna\")) #astimezone method\n", " dtobj_2=dtobj22.astimezone(pytz.timezone(\"Europe/Vienna\")) #astimezone method\n", "\n", " # t1 and t2 in local time as strings\n", " tta = dtobj_1.strftime(\"%Y-%m-%d %H:%M:%S.%f\")\n", " ttb = dtobj_2.strftime(\"%Y-%m-%d %H:%M:%S.%f\")\n", "\n", " # difference in seconds between time local and time UTC\n", " seco = float(calendar.timegm(time.strptime(tta, \"%Y-%m-%d %H:%M:%S.%f\"))-calendar.timegm(time.strptime(t1, \"%Y-%m-%d %H:%M:%S.%f\")))\n", " print(\"seco =\",seco)\n", "\n", " t1b = float(calendar.timegm(time.strptime(ta, \"%Y-%m-%d %H:%M:%S.%f\")))\n", " t2b = float(calendar.timegm(time.strptime(tb, \"%Y-%m-%d %H:%M:%S.%f\")))\n", "\n", "\n", " inc1='Inc1'\n", " inc2='Inc2'\n", " ref1='Ref1'\n", " ref2='Ref2'\n", "\n", "\n", " tt0,vv0=set1['Inc1']\n", " tt1,vv1=set1['Inc2']\n", "\n", " tt01,ref1=set1['Ref1']\n", " tt02,ref2=set1['Ref2']\n", "\n", " print(\"tto = \",tt0)\n", "\n", " # tt0 = tt0 - seco\n", " # tt1 = tt1 - seco\n", "\n", " return tt0,vv0,ref1,tt1,vv1,ref2" ] }, { "cell_type": "code", "execution_count": 11, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "IOPub data rate exceeded.\n", "The Jupyter server will temporarily stop sending output\n", "to the client in order to avoid crashing it.\n", "To change this limit, set the config variable\n", "`--ServerApp.iopub_data_rate_limit`.\n", "\n", "Current values:\n", "ServerApp.iopub_data_rate_limit=1000000.0 (bytes/sec)\n", "ServerApp.rate_limit_window=3.0 (secs)\n", "\n" ] } ], "source": [ "# Execution\n", "tt0_01,vv0_01,ref1_01,tt1_01,vv1_01,ref2_01 = fillvarpli(pli,t1,t2)\n", "\n", "\n", "first = 0\n", "second = int(len(tt0_01) - 1)\n", "\n", "primo = tt0_01[0]\n", "secondo = tt0_01[len(tt0_01)-1]\n", "\n", "majtk = len(vv0_01)/10/6\n", "mintk = majtk/4\n", "\n", "major_ticks = np.arange(tt0_01[first], tt0_01[second], majtk)\n", "minor_ticks = np.arange(tt0_01[first], tt0_01[second], mintk) " ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [] } ], "metadata": { "kernelspec": { "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.11.0" } }, "nbformat": 4, "nbformat_minor": 4 } ————END of code----------- 00:00:00.000 1717459200.000 0.078724480 0.039318143 0.048483948 0.131284533 0.063933287 0.052287658 0.061287437 0.103761961 00:00:00.033 1717459200.033 0.078592297 0.039438621 0.048571069 0.131187080 0.063932632 0.052287517 0.061286125 0.103762107 00:00:00.067 1717459200.067 0.078577040 0.039366136 0.048518060 0.131360571 0.063931897 0.052286136 0.061284330 0.103762236 00:00:00.100 1717459200.100 0.078572795 0.039294372 0.048501322 0.131458011 0.063930457 0.052286859 0.061287075 0.103763279 00:00:00.133 1717459200.133 0.079023172 0.039137271 0.048292120 0.131403456 0.063932890 0.052287624 0.061284528 0.103763038 00:00:00.167 1717459200.167 0.078505375 0.039542403 0.048597037 0.131128533 0.063934370 0.052288990 0.061287683 0.103763598 00:00:00.200 1717459200.200 0.078621849 0.039386922 0.048629364 0.131129838 0.063929251 0.052286659 0.061284553 0.103763449 00:00:00.233 1717459200.233 0.078781380 0.039234843 0.048413777 0.131401889 0.063928355 0.052285795 0.061285160 0.103764432 00:00:00.267 1717459200.267 0.078736263 0.039367673 0.048420775 0.131292070 0.063930897 0.052286868 0.061285622 0.103762605 00:00:00.300 1717459200.300 0.078614485 0.039462817 0.048522202 0.131202572 0.063928480 0.052287767 0.061284340 0.103763561

…

On 5 Jun 2024, at 13:54, Nicolas Holzschuch ***@***.***> wrote: I'm afraid the notebook does not appear here (github removes the pieces attached to e-mail) and I cannot download the data using the link provided either. — Reply to this email directly, view it on GitHub <#328 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BI6VT52AXAQNSWPEV2N2HGLZF34BBAVCNFSM6AAAAABI2JVZAOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNBZGY2DOMRTHA>. You are receiving this because you authored the thread.

[bdigirolamo]

It is connected to the size of the data file, I sorted it out. I simplified the code, now I have to figure out how to select a subset of data, thing that I was doing with the dictionary reading from an external database, but I have to rethink. Thanks anyway