.. DO NOT EDIT. .. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY. .. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE: .. "examples/plot_read_files_neo_io.py" .. LINE NUMBERS ARE GIVEN BELOW. .. only:: html .. note:: :class: sphx-glr-download-link-note :ref:`Go to the end ` to download the full example code. .. rst-class:: sphx-glr-example-title .. _sphx_glr_examples_plot_read_files_neo_io.py: Reading files with neo.io ========================= .. GENERATED FROM PYTHON SOURCE LINES 8-9 Start with package import and getting a datafile .. GENERATED FROM PYTHON SOURCE LINES 9-22 .. code-block:: Python import urllib import neo url_repo = "https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/raw/master/" # Plexon files distantfile = url_repo + "plexon/File_plexon_3.plx" localfile = "File_plexon_3.plx" urllib.request.urlretrieve(distantfile, localfile) .. rst-class:: sphx-glr-script-out .. code-block:: none ('File_plexon_3.plx', ) .. GENERATED FROM PYTHON SOURCE LINES 23-24 Now we can create our reader and read some data .. GENERATED FROM PYTHON SOURCE LINES 24-31 .. code-block:: Python # create a reader reader = neo.io.PlexonIO(filename="File_plexon_3.plx") # read the blocks blks = reader.read(lazy=False) print(blks) .. rst-class:: sphx-glr-script-out .. code-block:: none [] .. GENERATED FROM PYTHON SOURCE LINES 32-35 Once we have our blocks we can iterate through each block of data and see the contents of all parts of that data .. GENERATED FROM PYTHON SOURCE LINES 35-45 .. code-block:: Python # access to segments for blk in blks: for seg in blk.segments: print(seg) for asig in seg.analogsignals: print(asig) for st in seg.spiketrains: print(st) .. rst-class:: sphx-glr-script-out .. code-block:: none [[1630.8594] [1525.8789] [1389.1602] ... 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1.35112000e+01 1.35208667e+01 1.35313333e+01 1.35609333e+01 1.35714000e+01 1.36021333e+01 1.36112667e+01 1.36422667e+01 1.36512667e+01 1.36817333e+01 1.36913333e+01 1.37007333e+01 1.37114000e+01 1.37714000e+01 1.38113333e+01 1.38410667e+01 1.38515333e+01 1.38714000e+01 1.38806667e+01 1.39018000e+01 1.39115333e+01 1.39315333e+01 1.39419333e+01 1.39516000e+01 1.39714667e+01 1.39822000e+01 1.40018667e+01 1.40218000e+01 1.40316667e+01 1.40516000e+01 1.40716000e+01 1.40915333e+01 1.41109333e+01 1.41209333e+01 1.41316667e+01 1.41612667e+01 1.42012667e+01 1.42213333e+01 1.42423333e+01 1.42517333e+01 1.42609333e+01 1.43012667e+01 1.43116667e+01 1.43224667e+01 1.43316667e+01 1.43410667e+01 1.43518000e+01 1.43718000e+01 1.43824000e+01 1.44116667e+01 1.44318667e+01 1.44414000e+01 1.44517333e+01 1.44610000e+01 1.44717333e+01 1.44910667e+01 1.45021333e+01 1.45110667e+01 1.45318000e+01 1.45520000e+01 1.45919333e+01 1.46120000e+01 1.46415333e+01 1.46518667e+01 1.46615333e+01 1.46786667e+01 1.47015333e+01 1.47022000e+01 1.47120000e+01 1.47212000e+01 1.47320000e+01 1.47411333e+01 1.47424000e+01 1.47520667e+01 1.47720000e+01 1.48120000e+01 1.48320000e+01 1.48413333e+01 1.48520000e+01 1.48824000e+01 1.48919333e+01 1.49024667e+01 1.49120000e+01 1.49321333e+01 1.49520000e+01 1.49721333e+01 1.49828000e+01] s [ 0.15986667 0.33046667 0.44386667 2.1798 2.20106667 2.205 2.27426667 2.28026667 2.337 2.60246667 2.8548 3.01506667 3.69406667 3.90206667 3.96613333 4.06833333 4.75686667 8.24273333 8.40473333 8.40846667 8.94506667 9.06513333 9.4184 10.05866667 10.25626667 10.566 10.65906667 10.9338 12.0024 12.84006667 13.8206 14.17546667 14.77073333 14.7718 ] s [ 0.26393333 0.27193333 0.3628 0.36973333 0.37593333 0.4696 0.5218 0.54966667 0.58406667 2.16666667 2.19713333 2.19826667 2.20393333 2.2878 2.29126667 2.29266667 2.29446667 2.473 3.79186667 3.99573333 8.6804 8.6834 9.2844 10.4002 10.4014 10.74406667 11.08033333 11.2194 11.22626667 12.14466667 12.46126667 13.67673333 13.80913333 13.83426667 13.96873333 13.96986667] s [ 0.68666667 0.99346667 1.45386667 1.83406667 2.7546 2.93226667 3.5124 3.5152 3.83533333 4.65326667 5.29613333 7.94086667 8.57806667 8.63793333 8.64166667 8.94506667 9.07453333 9.2386 10.57793333 11.41946667 12.1506 12.28 12.6164 13.04133333 13.48053333 13.65813333 13.81133333 14.15046667 14.24113333 14.4384 ] s [ 0.35986667 1.21813333 1.95606667 2.14953333 2.29126667 2.337 2.63493333 3.77266667 5.25046667 8.3684 9.06506667 10.06846667 10.11886667 10.21333333 11.4234 12.00933333 12.04793333 13.1026 13.6744 ] s [ 3.7708 12.46126667] s [ 0.26386667 0.4602 0.53486667 0.54173333 0.582 0.65433333 0.69873333 0.83986667 0.86253333 1.7048 1.834 2.15053333 2.20493333 2.29126667 2.29346667 2.337 2.3874 3.77273333 3.7774 3.7846 3.7952 3.8468 4.31113333 4.83473333 5.4068 8.1856 8.2886 8.5178 8.64166667 9.76913333 10.23173333 10.519 10.74973333 11.35826667 11.4594 12.04806667 12.46126667 12.95106667 13.20226667 13.52166667 13.85193333 13.9714 ] s [ 0.3896 0.52293333 0.52433333 0.52926667 2.20006667 2.207 2.33946667 3.7774 5.02126667 8.966 10.43646667 13.83613333 13.85906667 13.86226667 13.8648 ] s [ 0.29646667 0.37346667 0.52413333 0.52813333 0.52946667 0.56793333 0.85413333 0.99346667 1.9256 2.1834 2.20006667 2.2014 2.205 2.21 2.30026667 2.30313333 2.30613333 2.30913333 2.3122 3.59946667 3.7728 3.84213333 3.9972 4.00526667 4.4624 8.0578 8.7846 9.07066667 9.17813333 9.60806667 10.1588 10.3342 10.34246667 10.3458 10.349 10.40833333 10.57893333 11.22666667 11.22973333 11.23126667 12.12173333 12.14106667 13.5504 13.5572 13.5694 13.67446667 13.6782 13.68013333 13.8342 13.85793333 13.86793333] s .. GENERATED FROM PYTHON SOURCE LINES 46-47 Let's look at another file type .. GENERATED FROM PYTHON SOURCE LINES 47-55 .. code-block:: Python # CED Spike2 files distantfile = url_repo + "spike2/File_spike2_1.smr" localfile = "./File_spike2_1.smr" urllib.request.urlretrieve(distantfile, localfile) # create a reader reader = neo.io.Spike2IO(filename="File_spike2_1.smr") .. GENERATED FROM PYTHON SOURCE LINES 56-58 Despite being a different raw file format we can access the data in the same way .. GENERATED FROM PYTHON SOURCE LINES 58-63 .. code-block:: Python # read the block bl = reader.read(lazy=False)[0] print(bl) .. rst-class:: sphx-glr-script-out .. code-block:: none .. GENERATED FROM PYTHON SOURCE LINES 64-66 Similarly we can view the different types of data within the block (AnalogSignals and SpikeTrains) .. GENERATED FROM PYTHON SOURCE LINES 66-74 .. code-block:: Python # access to segments for seg in bl.segments: print(seg) for asig in seg.analogsignals: print(asig) for st in seg.spiketrains: print(st) .. rst-class:: sphx-glr-script-out .. code-block:: none [[-0.05447388] [-0.07736207] [-0.09613039] ... [-0.219574 ] [-0.17303468] [-0.11978151]] V [234.03513 258.33255 261.00681 261.94305 262.84941 265.71789 270.25965 271.16601 282.83415 300.92151 302.78901 310.19427 324.14325 333.77955 337.40001 339.25257 343.82919 348.39087 349.32711 352.08603 419.71443 433.55883] s [226.89381 227.78025 230.43957 231.34095 236.64465 243.85071 244.74213 249.34863 250.22511 267.50571 268.40709 275.56833 276.47469 279.24855 284.72157 287.36595 288.24741 317.58957 327.90813 329.87523 330.78159 353.89377 363.28605 364.18245 368.83377 377.08563 378.89337 379.80969 384.47097 388.21593 391.07445 391.96587 392.85729 403.74357 408.40983 415.02327 415.94955 421.60683 428.88759] s [240.29499 242.07285 266.60433 272.90901 273.81537 274.67691 294.60189 296.39967 298.18749 358.56003 362.35479 367.93239 369.70527 383.54469 386.37333 400.15299 401.04939 401.95575 402.84219 407.49351 412.16475 416.95053 420.69549 424.38069 425.30199 426.19341 427.97625 430.76007 438.05079] s [221.65983 232.28217 233.14371 234.90663 237.53109 245.67837 246.60465 252.04779 253.86549 269.30847 278.35713 283.77537 297.30105 299.07891 299.99523 305.52303 322.28571 332.75865 338.32131 347.51439 350.22849 356.69751 361.40859 365.12865 367.00611 377.99199 389.17209 393.73875 405.66585 409.36101 410.27733 411.19365 414.06711 429.84873 436.29783 445.22697] s [225.99243 228.67167 264.73185 280.14993 285.65781 286.53429 289.16373 301.79301 311.11059 315.78681 316.69317 323.22195 331.72779 334.60125 335.49267 340.16889 341.10513 341.99655 342.87303 354.83001 355.73139 359.53113 360.40761 373.33569 374.24205 394.64511 395.54151 396.45285 413.10597 422.53809 432.63255 446.14329 447.02973] s [223.39785 307.45029 308.38155 309.29289 326.00079 326.96691 328.90413 345.73653 352.93761 372.40941 406.54233 439.87845] s [277.47567 291.05613 304.61169 320.47299 321.38433 357.67857 366.13461 370.61163 381.74691 390.16311 437.19423 443.43915] s [235.87773 238.52211 239.41851 253.04877 293.73039 319.56663 385.51677 423.53409 442.55271] s [247.56579 254.79675 303.71529 382.63833 417.87681 435.41139] s [290.13483 295.50327 314.88543 344.86005 351.17469 376.20417 438.98703 440.76489 441.65133 444.34053] s [222.46659 224.26437 225.13587 281.95767 318.55071 380.75091] s [306.58377 313.06773 371.51799 398.36019 399.26157] s [281.09613 336.45879 346.57815 375.21315 404.71965] s [291.95253 292.84395 312.16137 313.98903 325.15419 397.48371 434.52993] s [229.51827 241.16151 242.95929 248.45721 251.11155 255.68319 256.58955 257.45607 259.20903 260.11041 263.81553 272.05245 387.30957 418.78317 427.09479 431.70627] s .. rst-class:: sphx-glr-timing **Total running time of the script:** (0 minutes 13.712 seconds) .. _sphx_glr_download_examples_plot_read_files_neo_io.py: .. only:: html .. container:: sphx-glr-footer sphx-glr-footer-example .. container:: sphx-glr-download sphx-glr-download-jupyter :download:`Download Jupyter notebook: plot_read_files_neo_io.ipynb ` .. container:: sphx-glr-download sphx-glr-download-python :download:`Download Python source code: plot_read_files_neo_io.py ` .. only:: html .. rst-class:: sphx-glr-signature `Gallery generated by Sphinx-Gallery `_