diff --git a/jupyter_notebooks/smlm_challenge_2013_dao3d_2dfixed.ipynb b/jupyter_notebooks/smlm_challenge_2013_dao3d_2dfixed.ipynb index b4bf09bd..8cea5a63 100644 --- a/jupyter_notebooks/smlm_challenge_2013_dao3d_2dfixed.ipynb +++ b/jupyter_notebooks/smlm_challenge_2013_dao3d_2dfixed.ipynb @@ -82,32 +82,35 @@ "params = parameters.ParametersDAO()\n", "\n", "# Analyze the whole movie.\n", - "params.setAttr(\"max_frame\", \"int\", -1) \n", - "params.setAttr(\"start_frame\", \"int\", -1)\n", + "params.changeAttr(\"max_frame\", -1) \n", + "params.changeAttr(\"start_frame\", -1)\n", "\n", - "params.setAttr(\"background_sigma\", \"float\", 8.0)\n", + "params.changeAttr(\"background_sigma\", 8.0)\n", "\n", "# These were specified on the website for this dataset.\n", - "params.setAttr(\"camera_gain\", \"float\", 1.0)\n", - "params.setAttr(\"camera_offset\", \"float\", 100.0)\n", + "params.changeAttr(\"camera_gain\", 1.0)\n", + "params.changeAttr(\"camera_offset\", 100.0)\n", "\n", - "params.setAttr(\"find_max_radius\", \"int\", 5)\n", - "params.setAttr(\"foreground_sigma\", \"float\", 1.0)\n", - "params.setAttr(\"iterations\", \"int\", 20)\n", - "params.setAttr(\"model\", \"string\", \"2dfixed\")\n", - "params.setAttr(\"pixel_size\", \"float\", 100.0)\n", - "params.setAttr(\"roi_size\", \"int\", 9)\n", + "# Since this parameter can be either a float or an int we need\n", + "# to specify which type we want it to be.\n", + "params.changeAttr(\"find_max_radius\", 5, node_type = \"float\")\n", + "\n", + "params.changeAttr(\"foreground_sigma\", 1.0)\n", + "params.changeAttr(\"iterations\", 20)\n", + "params.changeAttr(\"model\", \"2dfixed\")\n", + "params.changeAttr(\"pixel_size\", 100.0)\n", + "params.changeAttr(\"roi_size\", 9)\n", "\n", "# Convert from FWHM in nanometers to sigma in pixels.\n", - "params.setAttr(\"sigma\", \"float\", 258.21/(100.0 * 2.355))\n", - "params.setAttr(\"threshold\", \"float\", 6)\n", + "params.changeAttr(\"sigma\", 258.21/(100.0 * 2.355))\n", + "params.changeAttr(\"threshold\", 6)\n", "\n", "# Don't do tracking.\n", - "params.setAttr(\"radius\", \"float\", \"0\")\n", - "params.setAttr(\"descriptor\", \"string\", \"1\")\n", + "params.changeAttr(\"radius\", \"0.0\")\n", + "params.changeAttr(\"descriptor\", \"1\")\n", "\n", "# Don't do drift-correction.\n", - "params.setAttr(\"drift_correction\", \"int\", 0)\n", + "params.changeAttr(\"drift_correction\", 0)\n", "\n", "params.toXMLFile(\"analysis.xml\", pretty = True)" ] @@ -141,28 +144,30 @@ "Reference results:\n", "\n", "```\n", - "Added 46444\n", - " 4708 peak finding iterations.\n", + "Added 46437\n", + " 4705 peak finding iterations.\n", "\n", " 0 fits reset due to Cholesky failure.\n", " 14 fits reset due to image margin.\n", " 677 fits reset due to negative value in fit function.\n", - " 115 fits reset due to negative height.\n", - " 534072 fits reset due to non-decreasing error (LM).\n", + " 110 fits reset due to negative height.\n", + " 533925 fits reset due to non-decreasing error (LM).\n", " 0 fits did not converge.\n", " 17 fits were lost.\n", " 415 peaks lost to proximity filter.\n", " 244 peaks lost to low significance.\n", - " 6711697 fitting iterations.\n", + " 6706925 fitting iterations.\n", "\n", "Tracking.\n", "\n", "Checking z values.\n", "\n", "Analysis complete\n", - "CPU times: user 55 s, sys: 171 ms, total: 55.1 s\n", - "Wall time: 55 s\n", - "```" + "CPU times: user 55.5 s, sys: 486 ms, total: 56 s\n", + "Wall time: 55.4 s\n", + "```\n", + "\n", + "Results may vary slightly. In particular the FFTW library is not completely deterministic when run with `FFTW_MEASURE`." ] }, {