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    "# FTICR-MS Processing and Display of Phase-Sensitive spectra\n",
    "\n",
    "### *This is a preliminary version - use with caution*\n",
    "\n",
    "a simplified environment for processing 1D Bruker FTICR datasets with `SPIKE`\n",
    "\n",
    "Run each python cell in sequence by using the ⇥Run button above (or typing *shift* Enter).\n",
    "\n",
    "Cells are meant to be used in order, taking you to the complete analysis, but you can go back at any time.\n",
    "\n",
    "### Initialization of the environment\n",
    "the following cell should be run only once, at the beginning of the processing"
   ]
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     "data": {
      "text/markdown": [
       "## STARTING Environment..."
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     "text": [
      "\n",
      "    ========================\n",
      "          SPIKE\n",
      "    ========================\n",
      "    Version     : 0.99.27\n",
      "    Date        : 27-07-2021\n",
      "    Revision Id : 518\n",
      "    ========================\n",
      "*** zoom3D not loaded ***\n",
      "plugins loaded:\n",
      "Fitter,  Linear_prediction,  Peaks,  bcorr,  fastclean,  gaussenh,  rem_ridge,  sane,  sg,  test,  urQRd, \n",
      "plugins loaded:\n",
      "msapmin, \n",
      "\n",
      "spike.plugins.report() for a short description of each plugins\n",
      "spike.plugins.report('module_name') for complete documentation on one plugin\n",
      "plugins loaded:\n",
      "FTMS_calib,  PhaseMS,  diagonal_2DMS, \n",
      "*** PALMA not loaded ***\n",
      "plugins loaded:\n",
      "Bruker_NMR_FT,  Bucketing,  Integrate,  apmin, \n",
      "\n",
      "Interactive module version, 1.2.1\n",
      "Run date: 2021-07-29T17:52:55.825220\n",
      "\n",
      "Interactive module version, 1.2.1\n"
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       "## ...program is Ready"
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    "# load all python and interactive tools - should be run only once\n",
    "from IPython.display import display, HTML, Markdown, Image\n",
    "display(Markdown('## STARTING Environment...'))\n",
    "import matplotlib as mpl\n",
    "%matplotlib widget\n",
    "import spike\n",
    "from spike.File import BrukerMS\n",
    "from spike.Interactive import INTER as I\n",
    "from spike.Interactive import FTICR_INTER as FI\n",
    "from spike.Interactive import INTER_MS as IMS\n",
    "from spike.Interactive.ipyfilechooser import FileChooser\n",
    "print(\"\\nInteractive module version,\",I.__version__)\n",
    "from datetime import datetime\n",
    "print('Run date:', datetime.now().isoformat() )\n",
    "I.initialize()\n",
    "display(Markdown('## ...program is Ready'))\n",
    "from importlib import reload  # this line is debugging help\n",
    "\n",
    "# configurable items\n",
    "mpl.rcParams['figure.figsize'] = (8,4)   # (X,Y) default figure size\n",
    "I.Activate_Wheel = True                  # True/False wheel control in the graphic cells "
   ]
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   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Choose the file\n",
    "Use `FileChooser()` to choose a file on your disk - The optional `base` argument, starts the exploration on a given location.\n",
    "\n",
    "Bruker files are named `fid` and are contained in a `*.d` directory."
   ]
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  {
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   "execution_count": 3,
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     "end_time": "2021-07-29T15:53:17.597908Z",
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       "FileChooser(path='/home/mad/Documents/spike/Notebooks', filename='', show_hidden='False')"
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   "source": [
    "FC = FileChooser(filetype='fid')\n",
    "display(FC)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "(After the selection, the selected filename is found in the `FC.selected` variable)\n",
    "### Import dataset\n"
   ]
  },
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   "cell_type": "code",
   "execution_count": 4,
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   "outputs": [
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     "text": [
      "Reading file  /DATA/DATA/FT-ICR/Zherebker_21_06_21/pos-Glutathione-internal_000001.d/fid\n",
      "Using 3 parameters calibration,  Warning calibB is -ML2\n"
     ]
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      "text/plain": [
       "FTICR data-set\n",
       "Bo: 7.05\n",
       "Single Spectrum data-set\n",
       "FT-ICR axis at 714.285714 kHz,  4194304 real points,  from physical mz =  151.655   to m/z = 1500.000  R max (M=400) = 1590317"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
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   "source": [
    "# This is simply done with the `Import_1D()` tool, which returns a `SPIKE` object.\n",
    "# We store it into a variable, evaluating the variable show a summary of the dataset. \n",
    "print('Reading file ',FC.selected)\n",
    "d1 = BrukerMS.Import_1D(FC.selected)\n",
    "d1.filename = FC.selected\n",
    "d1.set_unit('sec').display(title=FC.selected_path+\" transient\")\n",
    "d1"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### First Compute Modulus Spectrum\n",
    "\n",
    "many processing methods are available, they can be either applied one by one, or piped by chaining them.\n",
    "\n",
    "Here we are chaining  apodisation - zerofill - FT - modulus\n",
    "\n",
    "then setting to `m/z` unit (`Hz` and `points` also available) - finally `display()` is used to display the dataset.\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2021-07-29T15:54:48.262801Z",
     "start_time": "2021-07-29T15:54:45.724049Z"
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   "outputs": [
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       "Show1D(children=(VBox(children=(Button(button_style='success', description='Reset', layout=Layout(width='80px'…"
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     "output_type": "display_data"
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   "source": [
    "D1md = d1.copy() # copy the imported data-set to another object for processing\n",
    "D1md.kaiser(4).zf(4).rfft().modulus() # kaiser(4) is an apodisation well adapted to FTICR, slightly more resolution than hamming(\n",
    "D1md.set_unit('m/z')  # set to ppm unit - and display\n",
    "I.Show1D(D1md, title=FC.selected_path)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# the interactive phaser.\n",
    "\n",
    "we'll apply a phase correction $\\phi \\propto p_o + p_1 f_w + p_2 f_w^2$ where $f_w$ is the frequency of the FTICR signal across the spectral width\n",
    "\n",
    "$p_0$ is expressed in degrees, $p_1, p_2$ are expressed in number of of full turns over the spectral width.\n",
    "\n",
    "In interactive mode, there is also a $pivot$,  it is the location where P1 and P2 are inactive.\n",
    "It is a convenience for interaction,  P0 P1 and P2 are equal to $p_o, p_1$ and $p_2$ for $pivot=0$ i.e. on the left side.\n",
    "Moving the pivot modifies the interactive values of P0 and P1, don't worry.\n",
    "\n",
    "**Recipe**\n",
    "\n",
    "- 1/ start it below - spectrum is displayed in $Hz$\n",
    "    - a very rough first guess is already in place\n",
    "    - (optionally, set the values to zero)\n",
    "- 2/ zoom on a low frequency massive (on the left of the spectrum - corresponds to high masses)  \n",
    "    - a/ the chose zoom should be quite populated on a wide enough range - use scale on the side to have it full screen\n",
    "    - b/ right click on the center - this defines the pivot location\n",
    "    - c/ use P0 to put the central line in absorption\n",
    "    - d/ use P1 to extend the absorption zone as far as possible, try to be as precise as possible\n",
    "        - if possible, try to zoom out and continue extending\n",
    "    - e/ once it's Ok, click on **\"Add Entry\"**\n",
    "- 3/ zoom on a high frequency massive (low masses)\n",
    "    - redo steps a/ to d/ above\n",
    "    - once you're fine, you can click on **\"Add Entry\"**, this will modify the value of P2 automatically\n",
    "- 4/ redo step 3/ in many different location until is seems that you have a large zone in the middle of the spectrum which is phased.\n",
    "    - if you're lost, or if P2 does not stabilises, you can always clear the list, keeping the phase correction, but restarting the P2 computation.\n",
    "    - you can always restart the cell\n",
    "- 5/ now with the whole spectrum on the zoom, \n",
    "    - set the pivot in the center\n",
    "    - touch P0 to phase the center\n",
    "    - touch P1 to extend the phase region\n",
    "    - then slightly touch P2 to extend further the phased region\n",
    "- **Done**"
   ]
  },
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   "cell_type": "code",
   "execution_count": 7,
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     "start_time": "2021-07-29T15:57:49.396468Z"
    },
    "scrolled": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "initial values P1: 841   P2: 8204\n"
     ]
    },
    {
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      "text/plain": [
       "Phaser1D(children=(VBox(children=(HBox(children=(Button(button_style='success', description='Done', style=Butt…"
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   ],
   "source": [
    "simax = min(512*1024, d1.size1)\n",
    "D1ph = d1.copy()       # copy the imported data-set to another object for processing\n",
    "D1ph.apod_sq_sin(maxi=0).chsize(simax).zf(2).rfft()\n",
    "#D1ph.apod_sin(maxi=0.35).rfft()\n",
    "reload(IMS)\n",
    "print (\"initial values P1: %.0f   P2: %.0f\"%IMS.firstguess(d1))\n",
    "IMS.Phaser1D(D1ph.set_unit('Hz'), title=FC.selected_path);"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### And now compute the full version"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2021-05-29T08:33:57.439565Z",
     "start_time": "2021-05-29T08:33:57.307953Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "FTICR data-set\n",
       "Bo: 7.05\n",
       "Single Spectrum data-set\n",
       "FT-ICR axis at 535.714286 kHz,  1048576 real points,  from physical mz =  202.203   to m/z = 1500.000  R max (M=400) = 530100"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "D1 = d1.copy() # copy the imported data-set to another object for processing\n",
    "D1.apod_sin(maxi=0.15).zf(4).rfft()\n",
    "D1.phaseMS(D1ph.axis1.P0, D1ph.axis1.P1, D1ph.axis1.P2,0.0).real()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### baseline correction, and display"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2021-05-29T08:35:06.734762Z",
     "start_time": "2021-05-29T08:35:06.572236Z"
    }
   },
   "outputs": [
    {
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       "Canvas(toolbar=Toolbar(toolitems=[('Home', 'Reset original view', 'home', 'home'), ('Back', 'Back to previous …"
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    {
     "data": {
      "text/plain": [
       "FTICR data-set\n",
       "Bo: 7.05\n",
       "Single Spectrum data-set\n",
       "FT-ICR axis at 535.714286 kHz,  1048576 real points,  from physical mz =  202.203   to m/z = 1500.000  R max (M=400) = 530100"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from spike.plugins.bcorr import autopoints\n",
    "xp = autopoints(D1md, int(2*D1ph.axis1.P2))\n",
    "D1.bcorr(method='spline', xpoints=xp, nsmooth=2)\n",
    "D1.set_unit('m/z').display(title=FC.selected_path)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Compare phase-sensitive and modulus !"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2021-05-29T08:34:41.941148Z",
     "start_time": "2021-05-29T08:34:41.852174Z"
    }
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   "outputs": [
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    },
    {
     "data": {
      "text/plain": [
       "FTICR data-set\n",
       "Bo: 7.05\n",
       "Single Spectrum data-set\n",
       "FT-ICR axis at 535.714286 kHz,  1048576 real points,  from physical mz =  202.203   to m/z = 1500.000  R max (M=400) = 530100"
      ]
     },
     "execution_count": 13,
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   ],
   "source": [
    "D1.set_unit('m/z').display(title=FC.selected_path, label='phase-sensitive')\n",
    "D1md.set_unit('m/z').display(new_fig=False, label='modulus')\n",
    "#plt.scatter(D1bc.axis1.itomz(xp), D1bc.buffer[xp], marker='.', c='r')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
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