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    "\n",
    "# 2D NMR Processing and Display\n",
    "\n",
    "a simplified environment for processing 2D Bruker NMR 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",
    "The SPIKE code used for processing is visible in the cells, and can be used as a minimal tutorial.\n",
    "\n",
    "***Remark*** *to use this program, you should have installed the following packages:*\n",
    "\n",
    "- *a complete scientific python environment ( tested with python 3.7 - [anaconda](https://www.anaconda.com/))*\n",
    "- [`spike`](https://www.bitbucket.org/delsuc/spike) ( *version 0.99.21 minimum* )\n",
    "- [`ipywidgets`](https://ipywidgets.readthedocs.io/en/latest/)  ( *tested with version 7.6* )\n",
    "- [`ipyml`](https://github.com/matplotlib/jupyter-matplotlib)  ( *adds interactivity in the notebook* )\n",
    "\n",
    "## Initialization\n",
    "the following cell should be run only once, at the beginning of the processing"
   ]
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      "text/markdown": [
       "## STARTING Environment..."
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      "\n",
      "    ========================\n",
      "          SPIKE\n",
      "    ========================\n",
      "    Version     : 0.99.29\n",
      "    Date        : 20-09-2021\n",
      "    Revision Id : 529\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",
      "*** PALMA not loaded ***\n",
      "plugins loaded:\n",
      "Bruker_NMR_FT,  Bucketing,  Integrate,  apmin, \n",
      "\n",
      "Interactive module version, 1.2.1\n",
      "Run date: 2021-09-20T22:30:00.075239\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\n",
    "from __future__ import print_function, division\n",
    "from IPython.display import display, HTML, Markdown, Image\n",
    "display(Markdown('## STARTING Environment...'))\n",
    "import matplotlib.pyplot as plt\n",
    "import matplotlib as mpl\n",
    "%matplotlib widget\n",
    "import os.path as op\n",
    "import spike\n",
    "from spike.File.BrukerNMR import Import_2D\n",
    "from spike.Interactive import INTER as I\n",
    "from spike.Interactive import INTER_2D as I2D\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  # the two following lines are debugging help\n",
    "\n",
    "# configurable items - you may change them to fit you preferences\n",
    "verbose = 1                              # chose from 0 (terse) to 3 more verbose\n",
    "mpl.rcParams['figure.figsize'] = (8,4)   # (X,Y) default figure size\n",
    "I.Activate_Wheel = True                  # True/False    scale with wheel control in the graphic cells \n",
    "I.reverse_scroll = False                 # inverse the direction of the mouse wheel, whether it is `True` (TrackPad) or `False` (Mouse)"
   ]
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   "source": [
    "---\n",
    "\n",
    "### Choose the file\n",
    "The `FileChooser()` tool creates a dialog box which allows to choose a file on your disk\n",
    "\n",
    "- use the `Select` button\n",
    "- modify the ( *optional* ) `path` argument, to start the exploration on a given location\n",
    "- After the selection, the selected filename is found in `FC.selected`"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
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     "end_time": "2021-09-20T20:30:15.953190Z",
     "start_time": "2021-09-20T20:30:15.898772Z"
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       "FileChooser(path='/DATA', filename='ser', show_hidden='False')"
      ]
     },
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     "output_type": "display_data"
    }
   ],
   "source": [
    "FC = FileChooser(path='/DATA/',filename='ser')\n",
    "display(FC)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Import dataset\n",
    "\n",
    "This is simply done with the `Import_2D()` tool, which returns a `SPIKE` object.\n",
    "\n",
    "We store the dataset into a variable called d2. "
   ]
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     "end_time": "2021-09-20T20:30:24.413386Z",
     "start_time": "2021-09-20T20:30:24.095124Z"
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   "outputs": [
    {
     "name": "stdout",
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     "text": [
      "Reading file  /DATA/ARTEref/10/ser\n",
      "2D data-set\n",
      "Axis F1 :NMR axis at 700.163291 MHz, 256 complex pairs,  from -1.310430 ppm (-917.514982 Hz) to 10.711770 ppm  (7499.988138 Hz)\n",
      "Axis F2: NMR axis at 700.163291 MHz, 2048 complex pairs,  from -1.338538 ppm (-937.194868 Hz) to 10.683670 ppm  (7480.313549 Hz)\n",
      "data-set is hypercomplex (order 2)\n",
      "<cosydfph>\n"
     ]
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       "<b>title: </b>"
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       "Canvas(toolbar=Toolbar(toolitems=[('Home', 'Reset original view', 'home', 'home'), ('Back', 'Back to previous …"
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    "print('Reading file ',FC.selected)\n",
    "d2 = Import_2D(FC.selected)\n",
    "d2.filename = FC.selected\n",
    "d2.pulprog = d2.params['acqu']['$PULPROG']\n",
    "print(d2)                                      # print() of the dataset shows a summary of the parameters\n",
    "print(d2.pulprog)\n",
    "display(HTML('<b>title: </b>'+ d2.params['acqu']['title']))    # d1.params is a dictionary which contains the whole 'acqu' and 'proc' Bruker parameters\n",
    "#d2.set_unit('sec').display(title=\"%s %s\"%(FC.nmrname,d2.pulprog), scale='auto')\n",
    "plt.figure()\n",
    "plt.imshow(d2.get_buffer().real, cmap=\"seismic\");"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "*Check Proc1DNMR NoteBook for documentation on spectral display*\n",
    "\n",
    "## Basic Processing\n",
    "We are going to use a basic processing set-up, check the documentation for advanced processing\n",
    "\n",
    "### Fourier Transform - modulus mode!"
   ]
  },
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       "Show2D(children=(VBox(children=(HBox(children=(Checkbox(value=True, description='Positive', layout=Layout(widt…"
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       "<Figure size 872.727x872.727 with 4 Axes>"
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   "source": [
    "D2 = d2.copy() # copy the imported data-set to another object for processing\n",
    "# bk_ftF2 and bk_ftF1 (define in the Bruker plugin) find which FT to apply depending on FnMODE\n",
    "D2.apod_sin(maxi=0.5,axis='F2').zf(1,2).bk_ftF2()  # chaining  apodisation - zerofill - FT\n",
    "D2.apod_sin(maxi=0.5,axis='F1').zf(2,1).bk_ftF1()  # chaining  apodisation - zerofill - FT\n",
    "D2.modulus().set_unit('ppm').rem_ridge()\n",
    "#D2.display(scale=\"auto\", autoscalethresh=100.0, title=\"%s %s\"%(FC.nmrname,d2.pulprog))  # chain  set to ppm unit - and display\n",
    "I2D.Show2D(D2)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Advanced Phase sensitive processing\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
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     "end_time": "2021-09-20T20:31:02.816597Z",
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       "Show2D(children=(VBox(children=(HBox(children=(Checkbox(value=True, description='Positive', layout=Layout(widt…"
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   "source": [
    "D2ph = d2.copy() # copy the imported data-set to another object for processing\n",
    "# bk_ftF2 and bk_ftF1 (define in the Bruker plugin) find which FT to apply depending on FnMODE\n",
    "D2ph.apod_sin(maxi=0,axis='F2').zf(1,2).bk_ftF2().bk_pk()  # chaining  apodisation - zerofill - FT - phase\n",
    "D2ph.apod_sin(maxi=0,axis='F1').zf(2,1).bk_ftF1()  # chaining  apodisation - zerofill - FT\n",
    "D2ph.set_unit('ppm').rem_ridge()\n",
    "#D2.display(scale=\"auto\",  autoscalethresh=6.0, title=\"%s %s\"%(FC.nmrname,d2.pulprog))  # chain  set to ppm unit - and display\n",
    "S = I2D.Show2D(D2ph)           # note that you can create the view and store it in a var without displaying it\n",
    "S.negview.value = True         # and set some parameters (here negative view) before display\n",
    "S"
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   "source": [
    "### Rephasing\n",
    "\n",
    "Use the sliders to adjust the phase parameters,   the pivot can be set with a right click on the spectrum\n",
    "Top and Side spectra are taken at the pivot level.\n",
    "\n"
   ]
  },
  {
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       "Phaser2D(children=(VBox(children=(GridBox(children=(HTML(value='<b>F1</b>'), HTML(value='<b>F2</b>'), FloatSli…"
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   "source": [
    "reload(I2D)\n",
    "P = I2D.Phaser2D(D2ph)\n",
    "P"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# An interactive Display\n",
    "- show2D +\n",
    "- projections\n",
    "- color maps\n",
    "- title\n",
    "\n",
    "# todo\n",
    "- peak picking"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
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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": [
       "1D data-set\n",
       "Axis F1 :NMR axis at 700.163291 MHz, 4096 complex pairs,  from -1.338538 ppm (-937.194868 Hz) to 10.683670 ppm  (7480.313549 Hz)\n",
       "data-set is complex"
      ]
     },
     "execution_count": 22,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "F1slice = 3.3    # select a F1 (vertical) slice in current unit (here ppm) \n",
    "F2slice = 2.05   # select a F2 (horizontal) slice in current unit (here ppm) \n",
    "\n",
    "D2ph.col( D2ph.axis2.ctoi(F1slice)).display(title='F1 slice at F2=%.3f ppm'%(F1slice,))\n",
    "D2ph.row( D2ph.axis1.ctoi(F2slice)).display(title='F2 slice at F1=%.3f ppm'%(F2slice,))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "D2.set_unit('ppm')\n",
    "b = I2D.Show2D(D2.copy().real(axis='F1').real(axis='F2'), title=\"%s %s\"%(FC.nmrname,d2.pulprog))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Save on disk"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "D2.save('example1.gs2')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# The following entries or not finished yet"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Peak-Picker\n",
    "- moving the threshold determines the minimum peak intensity\n",
    "- peaks are searched only in the selected zoom window"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Export a bucket list"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# adapt the parameters below\n",
    "Zoom = ((0.5,8),(0.5,8))                    # zone to bucket       - in ppm\n",
    "BucketSize = (0.1,0.1)                 # width of the buckets - in ppm\n",
    "Output = 'screen'                   # 'screen'  or  'file'  determines output\n",
    "BucketFileName = 'bucket.csv'     #  the filename if Output (above) is 'file'  - don't forget the .csv extension."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# the following cell executes the bucketing\n",
    "if Output == 'file':\n",
    "    with open(BucketFileName,'w') as F:\n",
    "        D2.bucket2d(zoom=Zoom, bsize=BucketSize, file=F)\n",
    "    print('buckets written to %s\\n'%op.realpath(BucketFileName))\n",
    "else:\n",
    "    D2.bucket2d(zoom=Zoom, bsize=BucketSize)"
   ]
  },
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